From 328740c9f07114e50bc89875baa8bc68385db063 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 31 Aug 2023 12:13:53 -0400
Subject: [PATCH 01/49] handle local kraken2 db

---
 modules/local/kraken2_db_preparation.nf | 19 +++++++++++++++----
 1 file changed, 15 insertions(+), 4 deletions(-)

diff --git a/modules/local/kraken2_db_preparation.nf b/modules/local/kraken2_db_preparation.nf
index ebc9f912..78287f48 100644
--- a/modules/local/kraken2_db_preparation.nf
+++ b/modules/local/kraken2_db_preparation.nf
@@ -14,10 +14,21 @@ process KRAKEN2_DB_PREPARATION {
 
     script:
     """
-    mkdir db_tmp
-    tar -xf "${db}" -C db_tmp
-    mkdir database
-    mv `find db_tmp/ -name "*.k2d"` database/
+    if [[ -d ${db} ]]; then
+        if [[ ${db} != database ]]; then
+            ln -sr ${db} database
+        fi
+
+        # Make sure {hash,opts,taxo}.k2d are found in direcotry input
+        if [[ \$(find database/ -name "*.k2d" | wc -l) -lt 3 ]]; then
+            error "ERROR: Kraken2 requires '{hash,opts,taxo}.k2d' files."
+        fi
+    else
+        mkdir db_tmp
+        tar -xf "${db}" -C db_tmp
+        mkdir database
+        mv `find db_tmp/ -name "*.k2d"` database/
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 7f8909b7f2ca4be68fae1a073fcbd2d6d3d2179c Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 31 Aug 2023 12:14:37 -0400
Subject: [PATCH 02/49] handle local centrifuge db

---
 modules/local/centrifuge_db_preparation.nf | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/modules/local/centrifuge_db_preparation.nf b/modules/local/centrifuge_db_preparation.nf
index ecfbdb7b..b4926aff 100644
--- a/modules/local/centrifuge_db_preparation.nf
+++ b/modules/local/centrifuge_db_preparation.nf
@@ -14,7 +14,11 @@ process CENTRIFUGE_DB_PREPARATION {
 
     script:
     """
-    tar -xf "${db}"
+    if [[ -d ${db} ]]; then
+        ln -srf `find ${db}/ -type f -name "*.cf"` \${PWD}
+    else
+        tar -xf "${db}"
+    fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 118271c0d8eb66cf256336f6ad5ae49fc4b4da2e Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Tue, 5 Sep 2023 12:31:58 -0400
Subject: [PATCH 03/49] use busco_db and handle local and downloaded tar.gz
 files

---
 modules/local/busco.nf                | 21 +++++++------
 modules/local/busco_db_preparation.nf |  5 ++-
 modules/local/busco_summary.nf        |  5 +--
 subworkflows/local/busco_qc.nf        | 45 +++++++++++++++++++++------
 subworkflows/local/gtdbtk.nf          |  2 +-
 workflows/mag.nf                      | 18 +++--------
 6 files changed, 57 insertions(+), 39 deletions(-)

diff --git a/modules/local/busco.nf b/modules/local/busco.nf
index 9cf4b4ce..d009c6ba 100644
--- a/modules/local/busco.nf
+++ b/modules/local/busco.nf
@@ -8,8 +8,7 @@ process BUSCO {
 
     input:
     tuple val(meta), path(bin)
-    path(db)
-    path(download_folder)
+    tuple val(db_meta), path(db)
 
     output:
     tuple val(meta), path("short_summary.domain.*.${bin}.txt")          , optional:true , emit: summary_domain
@@ -25,17 +24,19 @@ process BUSCO {
 
     script:
     def cp_augustus_config = workflow.profile.toString().indexOf("conda") != -1 ? "N" : "Y"
-    def lineage_dataset_provided = params.busco_reference ? "Y" : "N"
+    def lineage_dataset_provided = "${db_meta.lineage}"
     def busco_clean = params.busco_clean ? "Y" : "N"
 
-    def p = "--auto-lineage"
-    if (params.busco_reference){
-        p = "--lineage_dataset dataset/${db}"
+    def p = ""
+    if ( "${lineage_dataset_provided}" == "Y" ) {
+        p += "--lineage_dataset dataset/${db}"
     } else {
-        if (params.busco_auto_lineage_prok)
-            p = "--auto-lineage-prok"
-        if (params.busco_download_path)
-            p += " --offline --download_path ${download_folder}"
+        p = "--offline --download_path ${db}"
+        if (params.busco_auto_lineage_prok) {
+            p += " --auto-lineage-prok"
+        } else {
+            p += " --auto-lineage"
+        }
     }
     """
     run_busco.sh "${p}" "${cp_augustus_config}" "${db}" "${bin}" ${task.cpus} "${lineage_dataset_provided}" "${busco_clean}"
diff --git a/modules/local/busco_db_preparation.nf b/modules/local/busco_db_preparation.nf
index b78133a5..a56a5af6 100644
--- a/modules/local/busco_db_preparation.nf
+++ b/modules/local/busco_db_preparation.nf
@@ -10,9 +10,8 @@ process BUSCO_DB_PREPARATION {
     path database
 
     output:
-    path "buscodb/*"    , emit: db
-    path database       , emit: database
-    path "versions.yml" , emit: versions
+    tuple val("${database.toString().replace(".tar.gz", "")}"), path("buscodb/*"), emit: db
+    path "versions.yml"                                                         , emit: versions
 
     script:
     """
diff --git a/modules/local/busco_summary.nf b/modules/local/busco_summary.nf
index c4023276..9ed758e2 100644
--- a/modules/local/busco_summary.nf
+++ b/modules/local/busco_summary.nf
@@ -15,11 +15,12 @@ process BUSCO_SUMMARY {
     path "versions.yml"     , emit: versions
 
     script:
-    def auto = params.busco_reference ? "" : "-a"
+    def reference = "${params.busco_db.toString().contains('odb10')}"
+    def auto = reference ? "" : "-a"
     def ss = summaries_specific.sort().size() > 0 ? "-ss ${summaries_specific}" : ""
     def sd = summaries_domain.sort().size() > 0 ? "-sd ${summaries_domain}" : ""
     def f = ""
-    if (!params.busco_reference && failed_bins.sort().size() > 0)
+    if ("${reference}" == false && failed_bins.sort().size() > 0)
         f = "-f ${failed_bins}"
     """
     summary_busco.py $auto $ss $sd $f -o busco_summary.tsv
diff --git a/subworkflows/local/busco_qc.nf b/subworkflows/local/busco_qc.nf
index 6165be47..eb93703a 100644
--- a/subworkflows/local/busco_qc.nf
+++ b/subworkflows/local/busco_qc.nf
@@ -9,23 +9,48 @@ include { BUSCO_SUMMARY                   } from '../../modules/local/busco_summ
 
 workflow BUSCO_QC {
     take:
-    busco_db_file           // channel: path
-    busco_download_folder   // channel: path
-    bins                    // channel: [ val(meta), path(bin) ]
+    busco_db   // channel: path
+    bins       // channel: [ val(meta), path(bin) ]
 
     main:
-    if (params.busco_reference){
-        BUSCO_DB_PREPARATION ( busco_db_file )
-        ch_busco_db = BUSCO_DB_PREPARATION.out.db
+    if ( busco_db.extension == 'gz' ) {
+        // Expects to be tar.gz!
+        BUSCO_DB_PREPARATION ( busco_db )
+
+        ch_db_for_busco = BUSCO_DB_PREPARATION.out.db
+                            .map{
+                                meta, db ->
+                                    def meta_new = [:]
+                                    meta_new['id'] = meta
+                                    meta_new['lineage'] = 'Y'
+                                    [ meta_new, db ]
+                            }
+    } else if ( busco_db.isDirectory() ) {
+        // Set meta to match expected channel cardinality for BUSCO
+        ch_db_for_busco = Channel
+                        .of(busco_db)
+                        .map{
+                            db ->
+                                def meta = [:]
+                                meta['id'] = db.toString().split('/').last()
+                                if ("${meta['id'].toString().contains('odb10')}" == true) {
+                                    meta['lineage'] = 'Y'
+                                } else {
+                                    meta['lineage'] = 'N'
+                                }
+                                [ meta, db ]
+                        }
+                        .collect()
     } else {
-        ch_busco_db = Channel.empty()
+        error("Unsupported object given to --busco_db, database must be supplied as either a directory or a .tar.gz file!")
     }
+
     BUSCO (
         bins,
-        ch_busco_db.collect().ifEmpty([]),
-        busco_download_folder.collect().ifEmpty([])
+        ch_db_for_busco
     )
-    if (params.save_busco_reference){
+
+    if (params.save_busco_db){
         // publish files downloaded by Busco
         ch_downloads = BUSCO.out.busco_downloads.groupTuple().map{lin,downloads -> downloads[0]}.toSortedList().flatten()
         BUSCO_SAVE_DOWNLOAD ( ch_downloads )
diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
index 21823962..f8020aa3 100644
--- a/subworkflows/local/gtdbtk.nf
+++ b/subworkflows/local/gtdbtk.nf
@@ -24,7 +24,7 @@ workflow GTDBTK {
                         def completeness  = -1
                         def contamination = -1
                         def missing, duplicated
-                        if (params.busco_reference) {
+                        if (params.busco_db.toString().contains('odb10')) {
                             missing    = row.'%Missing (specific)'      // TODO or just take '%Complete'?
                             duplicated = row.'%Complete and duplicated (specific)'
                         } else {
diff --git a/workflows/mag.nf b/workflows/mag.nf
index 11be8584..09e4119e 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -31,7 +31,7 @@ log.info logo + paramsSummaryLog(workflow) + citation
 WorkflowMag.initialise(params, log, hybrid)
 
 // Check input path parameters to see if they exist
-def checkPathParamList = [ params.input, params.multiqc_config, params.phix_reference, params.host_fasta, params.centrifuge_db, params.kraken2_db, params.cat_db, params.krona_db, params.gtdb_db, params.lambda_reference, params.busco_reference ]
+def checkPathParamList = [ params.input, params.multiqc_config, params.phix_reference, params.host_fasta, params.centrifuge_db, params.kraken2_db, params.cat_db, params.krona_db, params.gtdb_db, params.lambda_reference, params.busco_db ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 /*
@@ -145,17 +145,10 @@ if ( params.host_genome ) {
     ch_host_fasta = Channel.empty()
 }
 
-if(params.busco_reference){
-    ch_busco_db_file = Channel
-        .value(file( "${params.busco_reference}" ))
+if(params.busco_db){
+    ch_busco_db = file( "${params.busco_db}", checkIfExists: true )
 } else {
-    ch_busco_db_file = Channel.empty()
-}
-if (params.busco_download_path) {
-    ch_busco_download_folder = Channel
-        .value(file( "${params.busco_download_path}" ))
-} else {
-    ch_busco_download_folder = Channel.empty()
+    ch_busco_db = []
 }
 
 if(params.checkm_db) {
@@ -805,8 +798,7 @@ workflow MAG {
             */
 
             BUSCO_QC (
-                ch_busco_db_file,
-                ch_busco_download_folder,
+                ch_busco_db,
                 ch_input_bins_for_qc
             )
             ch_busco_summary = BUSCO_QC.out.summary

From d4b6258399503c8b996e3de1c7bf453ce04e6b05 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Tue, 5 Sep 2023 12:37:58 -0400
Subject: [PATCH 04/49] update information about kraken, centrifuge, and busco
 databases

---
 conf/test.config                |  2 +-
 conf/test_adapterremoval.config |  2 +-
 conf/test_ancient_dna.config    |  2 +-
 conf/test_bbnorm.config         |  2 +-
 conf/test_binrefinement.config  |  2 +-
 conf/test_full.config           |  2 +-
 conf/test_host_rm.config        |  2 +-
 conf/test_hybrid.config         |  4 ++--
 docs/output.md                  |  8 ++++----
 docs/usage.md                   |  2 +-
 lib/WorkflowMag.groovy          | 13 ++-----------
 nextflow.config                 |  5 ++---
 nextflow_schema.json            | 19 +++++++------------
 13 files changed, 25 insertions(+), 40 deletions(-)

diff --git a/conf/test.config b/conf/test.config
index 348b95d5..9c93278f 100644
--- a/conf/test.config
+++ b/conf/test.config
@@ -26,7 +26,7 @@ params {
     skip_krona                    = true
     min_length_unbinned_contigs   = 1
     max_unbinned_contigs          = 2
-    busco_reference               = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_db                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
     busco_clean                   = true
     skip_gtdbtk                   = true
     skip_concoct                  = true
diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config
index 92d51aec..d8bd581a 100644
--- a/conf/test_adapterremoval.config
+++ b/conf/test_adapterremoval.config
@@ -27,7 +27,7 @@ params {
     skip_krona                  = true
     min_length_unbinned_contigs = 1
     max_unbinned_contigs        = 2
-    busco_reference             = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_db                    = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
     skip_gtdbtk                 = true
     clip_tool                   = 'adapterremoval'
     skip_concoct                = true
diff --git a/conf/test_ancient_dna.config b/conf/test_ancient_dna.config
index 325362fc..ea672651 100644
--- a/conf/test_ancient_dna.config
+++ b/conf/test_ancient_dna.config
@@ -26,7 +26,7 @@ params {
     skip_krona                           = true
     min_length_unbinned_contigs          = 1
     max_unbinned_contigs                 = 2
-    busco_reference                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_db                             = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
     skip_gtdbtk                          = true
     ancient_dna                          = true
     binning_map_mode                     = 'own'
diff --git a/conf/test_bbnorm.config b/conf/test_bbnorm.config
index 5f481adf..55d48a8b 100644
--- a/conf/test_bbnorm.config
+++ b/conf/test_bbnorm.config
@@ -32,7 +32,7 @@ params {
     skip_krona                    = true
     min_length_unbinned_contigs   = 1
     max_unbinned_contigs          = 2
-    busco_reference               = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_db                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
     busco_clean                   = true
     skip_gtdbtk                   = true
     bbnorm                        = true
diff --git a/conf/test_binrefinement.config b/conf/test_binrefinement.config
index 85dda8db..bc1796d5 100644
--- a/conf/test_binrefinement.config
+++ b/conf/test_binrefinement.config
@@ -27,7 +27,7 @@ params {
     skip_krona                    = true
     min_length_unbinned_contigs   = 1
     max_unbinned_contigs          = 2
-    busco_reference               = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_db                      = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
     skip_gtdbtk                   = true
     refine_bins_dastool           = true
     refine_bins_dastool_threshold = 0
diff --git a/conf/test_full.config b/conf/test_full.config
index 4917332e..ea694247 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -28,7 +28,7 @@ params {
     spades_fix_cpus       = 10
     spadeshybrid_fix_cpus = 10
     megahit_fix_cpu_1     = true
-    // available options to enable reproducibility for BUSCO (--busco_download_path or --busco_reference) not used here
+    // available options to enable reproducibility for BUSCO (--busco_db) not used here
     // to allow detection of possible problems in automated lineage selection mode using public databases
 
     // test CAT with official taxonomic ranks only
diff --git a/conf/test_host_rm.config b/conf/test_host_rm.config
index b3487c6b..7af3bcd4 100644
--- a/conf/test_host_rm.config
+++ b/conf/test_host_rm.config
@@ -24,7 +24,7 @@ params {
     input                       = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.host_rm.csv'
     min_length_unbinned_contigs = 1
     max_unbinned_contigs        = 2
-    busco_reference             = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    busco_db                    = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
     skip_gtdbtk                 = true
     skip_concoct                = true
 }
diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config
index bc22d3d2..0600c88c 100644
--- a/conf/test_hybrid.config
+++ b/conf/test_hybrid.config
@@ -23,7 +23,7 @@ params {
     input                       = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.hybrid.csv'
     min_length_unbinned_contigs = 1
     max_unbinned_contigs        = 2
-    busco_reference             = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
-    skip_gtdbtk                   = true
+    busco_db                    = "https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz"
+    skip_gtdbtk                 = true
     skip_concoct                = true
 }
diff --git a/docs/output.md b/docs/output.md
index 902d0f12..8c56a713 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -484,7 +484,7 @@ For each bin or refined bin the median sequencing depth is computed based on the
 
 #### BUSCO
 
-[BUSCO](https://busco.ezlab.org/) is a tool used to assess the completeness of a genome assembly. It is run on all the genome bins and high quality contigs obtained by the applied binning and/or binning refinement methods (depending on the `--postbinning_input` parameter). By default, BUSCO is run in automated lineage selection mode in which it first tries to select the domain and then a more specific lineage based on phylogenetic placement. If available, result files for both the selected domain lineage and the selected more specific lineage are placed in the output directory. If a lineage dataset is specified already with `--busco_reference`, only results for this specific lineage will be generated.
+[BUSCO](https://busco.ezlab.org/) is a tool used to assess the completeness of a genome assembly. It is run on all the genome bins and high quality contigs obtained by the applied binning and/or binning refinement methods (depending on the `--postbinning_input` parameter). By default, BUSCO is run in automated lineage selection mode in which it first tries to select the domain and then a more specific lineage based on phylogenetic placement. If available, result files for both the selected domain lineage and the selected more specific lineage are placed in the output directory. If a lineage dataset is specified already with `--busco_db`, only results for this specific lineage will be generated.
 
 <details markdown="1">
 <summary>Output files</summary>
@@ -493,21 +493,21 @@ For each bin or refined bin the median sequencing depth is computed based on the
   - `[assembler]-[bin]_busco.log`: Log file containing the standard output of BUSCO.
   - `[assembler]-[bin]_busco.err`: File containing potential error messages returned from BUSCO.
   - `short_summary.domain.[lineage].[assembler]-[bin].txt`: BUSCO summary of the results for the selected domain when run in automated lineage selection mode. Not available for bins for which a viral lineage was selected.
-  - `short_summary.specific_lineage.[lineage].[assembler]-[bin].txt`: BUSCO summary of the results in case a more specific lineage than the domain could be selected or for the lineage provided via `--busco_reference`.
+  - `short_summary.specific_lineage.[lineage].[assembler]-[bin].txt`: BUSCO summary of the results in case a more specific lineage than the domain could be selected or for the lineage provided via `--busco_db`.
   - `[assembler]-[bin]_buscos.[lineage].fna.gz`: Nucleotide sequence of all identified BUSCOs for used lineages (domain or specific).
   - `[assembler]-[bin]_buscos.[lineage].faa.gz`: Aminoacid sequence of all identified BUSCOs for used lineages (domain or specific).
   - `[assembler]-[bin]_prodigal.gff`: Genes predicted with Prodigal.
 
 </details>
 
-If the parameter `--save_busco_reference` is set, additionally the used BUSCO lineage datasets are stored in the output directory.
+If the parameter `--save_busco_db` is set, additionally the used BUSCO lineage datasets are stored in the output directory.
 
 <details markdown="1">
 <summary>Output files</summary>
 
 - `GenomeBinning/QC/BUSCO/`
   - `busco_downloads/`: All files and lineage datasets downloaded by BUSCO when run in automated lineage selection mode. (Can currently not be used to reproduce analysis, see the [nf-core/mag website documentation](https://nf-co.re/mag/usage#reproducibility) how to achieve reproducible BUSCO results).
-  - `reference/*.tar.gz`: BUSCO reference lineage dataset that was provided via `--busco_reference`.
+  - `reference/*.tar.gz`: BUSCO reference lineage dataset that was provided via `--busco_db`.
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index f61f5621..45b8fa6c 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -187,7 +187,7 @@ You can fix this by using the prameter `--megahit_fix_cpu_1`. In both cases, do
 
 MetaBAT2 is run by default with a fixed seed within this pipeline, thus producing reproducible results.
 
-To allow also reproducible bin QC with BUSCO, run BUSCO providing already downloaded lineage datasets with `--busco_download_path` (BUSCO will be run using automated lineage selection in offline mode) or provide a specific lineage dataset via `--busco_reference` and use the parameter `--save_busco_reference`. This may be useful since BUSCO datasets are frequently updated and old versions do not always remain (easily) accessible.
+To allow also reproducible bin QC with BUSCO, run BUSCO providing already downloaded lineage datasets (BUSCO will be run using automated lineage selection in offline mode) or provide a specific lineage dataset via `--busco_db` and use the parameter `--save_busco_db`. This may be useful since BUSCO datasets are frequently updated and old versions do not always remain (easily) accessible.
 
 For the taxonomic bin classification with [CAT](https://github.com/dutilh/CAT), when running the pipeline with `--cat_db_generate` the parameter `--save_cat_db` can be used to also save the generated database to allow reproducibility in future runs. Note that when specifying a pre-built database with `--cat_db`, currently the database can not be saved.
 
diff --git a/lib/WorkflowMag.groovy b/lib/WorkflowMag.groovy
index 51822e4e..c290ecbf 100755
--- a/lib/WorkflowMag.groovy
+++ b/lib/WorkflowMag.groovy
@@ -102,22 +102,13 @@ class WorkflowMag {
             Nextflow.error('Both --skip_binqc and --binqc_tool \'checkm\' are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool.')
         }
         if (params.skip_binqc) {
-            if (params.busco_reference) {
-                Nextflow.error('Both --skip_binqc and --busco_reference are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_reference.')
-            }
-            if (params.busco_download_path) {
-                Nextflow.error('Both --skip_binqc and --busco_download_path are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_download_path.')
+            if (params.busco_db) {
+                Nextflow.error('Both --skip_binqc and --busco_db are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_db.')
             }
             if (params.busco_auto_lineage_prok) {
                 Nextflow.error('Both --skip_binqc and --busco_auto_lineage_prok are specified! Invalid combination, please specify either --skip_binqc or --binqc_tool \'busco\' with --busco_auto_lineage_prok.')
             }
         }
-        if (params.busco_reference && params.busco_download_path) {
-            Nextflow.error('Both --busco_reference and --busco_download_path are specified! Invalid combination, please specify either --busco_reference or --busco_download_path.')
-        }
-        if (params.busco_auto_lineage_prok && params.busco_reference) {
-            Nextflow.error('Both --busco_auto_lineage_prok and --busco_reference are specified! Invalid combination, please specify either --busco_auto_lineage_prok or --busco_reference.')
-        }
 
         if (params.skip_binqc && !params.skip_gtdbtk) {
             log.warn '--skip_binqc is specified, but --skip_gtdbtk is explictly set to run! GTDB-tk will be omitted because GTDB-tk bin classification requires bin filtering based on BUSCO or CheckM QC results to avoid GTDB-tk errors.'
diff --git a/nextflow.config b/nextflow.config
index 0ac8d964..329f70ad 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -121,10 +121,9 @@ params {
     // Bin QC
     skip_binqc                           = false
     binqc_tool                           = 'busco'
-    busco_reference                      = null
-    busco_download_path                  = null
+    busco_db                             = null
     busco_auto_lineage_prok              = false
-    save_busco_reference                 = false
+    save_busco_db                        = false
     busco_clean                          = false
     checkm_download_url                  = "https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz"
     checkm_db                            = null
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 5dbd2a26..85fce7c1 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -481,12 +481,12 @@
                 "centrifuge_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with centrifuge.",
-                    "help_text": "E.g. ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz."
+                    "help_text": "Local directory containing `*.cf` files or path to download compressed tar archive. E.g. ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz."
                 },
                 "kraken2_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with kraken2.",
-                    "help_text": "The database file must be a compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz."
+                    "help_text": "Local directory or compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz."
                 },
                 "krona_db": {
                     "type": "string",
@@ -757,23 +757,18 @@
                     "description": "Specify which tool for bin quality-control validation to use.",
                     "enum": ["busco", "checkm"]
                 },
-                "busco_reference": {
+                "busco_db": {
                     "type": "string",
-                    "description": "Download path for BUSCO lineage dataset, instead of using automated lineage selection.",
-                    "help_text": "E.g. https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz. Available databases are listed here: https://busco-data.ezlab.org/v5/data/lineages/."
-                },
-                "busco_download_path": {
-                    "type": "string",
-                    "description": "Path to local folder containing already downloaded and unpacked lineage datasets.",
-                    "help_text": "If provided, BUSCO analysis will be run in offline mode. Data can be downloaded from https://busco-data.ezlab.org/v5/data/ (files still need to be unpacked manually). Run in combination with automated lineage selection."
+                    "description": "Download path for BUSCO lineage dataset or path to local directory containing already downloaded and unpacked lineage datasets.",
+                    "help_text": "E.g. https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz or '/path/to/buscodb' (files still need to be unpacked manually). Available databases are listed here: https://busco-data.ezlab.org/v5/data/lineages/."
                 },
                 "busco_auto_lineage_prok": {
                     "type": "boolean",
                     "description": "Run BUSCO with automated lineage selection, but ignoring eukaryotes (saves runtime)."
                 },
-                "save_busco_reference": {
+                "save_busco_db": {
                     "type": "boolean",
-                    "description": "Save the used BUSCO lineage datasets provided via --busco_reference or downloaded when not using --busco_reference or --busco_download_path.",
+                    "description": "Save the used BUSCO lineage datasets provided via `--busco_db`.",
                     "help_text": "Useful to allow reproducibility, as BUSCO datasets are frequently updated and old versions do not always remain accessible."
                 },
                 "busco_clean": {

From 4304cf6947529b1542f15a2c7497ed9b17632747 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Fri, 15 Sep 2023 12:52:06 -0400
Subject: [PATCH 05/49] update parameter handling

---
 modules/local/busco.nf         | 13 +++++--------
 modules/local/busco_summary.nf |  2 +-
 2 files changed, 6 insertions(+), 9 deletions(-)

diff --git a/modules/local/busco.nf b/modules/local/busco.nf
index d009c6ba..ab1c5917 100644
--- a/modules/local/busco.nf
+++ b/modules/local/busco.nf
@@ -27,16 +27,13 @@ process BUSCO {
     def lineage_dataset_provided = "${db_meta.lineage}"
     def busco_clean = params.busco_clean ? "Y" : "N"
 
-    def p = ""
+    def p = params.busco_auto_lineage_prok ? "--auto-lineage-prok" : "--auto-lineage"
     if ( "${lineage_dataset_provided}" == "Y" ) {
-        p += "--lineage_dataset dataset/${db}"
+        p = "--lineage_dataset dataset/${db}"
+    } else if ( "${lineage_dataset_provided}" == "N" ) {
+        p += "--offline --download_path ${db}"
     } else {
-        p = "--offline --download_path ${db}"
-        if (params.busco_auto_lineage_prok) {
-            p += " --auto-lineage-prok"
-        } else {
-            p += " --auto-lineage"
-        }
+        lineage_dataset_provided = ""
     }
     """
     run_busco.sh "${p}" "${cp_augustus_config}" "${db}" "${bin}" ${task.cpus} "${lineage_dataset_provided}" "${busco_clean}"
diff --git a/modules/local/busco_summary.nf b/modules/local/busco_summary.nf
index 9ed758e2..e5015387 100644
--- a/modules/local/busco_summary.nf
+++ b/modules/local/busco_summary.nf
@@ -15,7 +15,7 @@ process BUSCO_SUMMARY {
     path "versions.yml"     , emit: versions
 
     script:
-    def reference = "${params.busco_db.toString().contains('odb10')}"
+    def reference = params.busco_db.toString().contains('odb10')
     def auto = reference ? "" : "-a"
     def ss = summaries_specific.sort().size() > 0 ? "-ss ${summaries_specific}" : ""
     def sd = summaries_domain.sort().size() > 0 ? "-sd ${summaries_domain}" : ""

From 190129e48ea836d72adf2e06abc9a6324ce11290 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Fri, 15 Sep 2023 12:53:43 -0400
Subject: [PATCH 06/49] set busco_db input as a path channel

---
 workflows/mag.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/workflows/mag.nf b/workflows/mag.nf
index 09e4119e..061a3734 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -145,8 +145,8 @@ if ( params.host_genome ) {
     ch_host_fasta = Channel.empty()
 }
 
-if(params.busco_db){
-    ch_busco_db = file( "${params.busco_db}", checkIfExists: true )
+if (params.busco_db) {
+    ch_busco_db = file(params.busco_db, checkIfExists: true)
 } else {
     ch_busco_db = []
 }

From 1961247b6fb73deda49038e2dfdfac134025e060 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Fri, 15 Sep 2023 12:58:17 -0400
Subject: [PATCH 07/49] handle busco_db inputs and allow for busco to auto
 download lineages

---
 subworkflows/local/busco_qc.nf | 63 +++++++++++++++++++---------------
 1 file changed, 36 insertions(+), 27 deletions(-)

diff --git a/subworkflows/local/busco_qc.nf b/subworkflows/local/busco_qc.nf
index eb93703a..4c00436b 100644
--- a/subworkflows/local/busco_qc.nf
+++ b/subworkflows/local/busco_qc.nf
@@ -13,36 +13,45 @@ workflow BUSCO_QC {
     bins       // channel: [ val(meta), path(bin) ]
 
     main:
-    if ( busco_db.extension == 'gz' ) {
-        // Expects to be tar.gz!
-        BUSCO_DB_PREPARATION ( busco_db )
+    if ( !busco_db.isEmpty() ) {
+        if ( busco_db.extension == "gz" ) {
+            // Expects to be tar.gz!
+            BUSCO_DB_PREPARATION ( busco_db )
 
-        ch_db_for_busco = BUSCO_DB_PREPARATION.out.db
-                            .map{
-                                meta, db ->
-                                    def meta_new = [:]
-                                    meta_new['id'] = meta
-                                    meta_new['lineage'] = 'Y'
-                                    [ meta_new, db ]
-                            }
-    } else if ( busco_db.isDirectory() ) {
-        // Set meta to match expected channel cardinality for BUSCO
-        ch_db_for_busco = Channel
-                        .of(busco_db)
-                        .map{
-                            db ->
-                                def meta = [:]
-                                meta['id'] = db.toString().split('/').last()
-                                if ("${meta['id'].toString().contains('odb10')}" == true) {
-                                    meta['lineage'] = 'Y'
-                                } else {
-                                    meta['lineage'] = 'N'
+            ch_db_for_busco = BUSCO_DB_PREPARATION.out.db
+                                .map{
+                                    meta, db ->
+                                        def meta_new = [:]
+                                        meta_new['id'] = meta
+                                        meta_new['lineage'] = 'Y'
+                                        [ meta_new, db ]
+                                }
+        } else if ( busco_db.isDirectory() ) {
+            // Set meta to match expected channel cardinality for BUSCO
+            ch_db_for_busco = busco_db
+                                .map{
+                                    db ->
+                                        def meta = [:]
+                                        meta['id'] = db.toString().split('/').last()
+                                        if ("${meta['id'].toString().contains('odb10')}" == true) {
+                                            meta['lineage'] = 'Y'
+                                        } else {
+                                            meta['lineage'] = 'N'
+                                        }
+                                        [ meta, db ]
                                 }
-                                [ meta, db ]
-                        }
-                        .collect()
+                                .collect()
+        }
     } else {
-        error("Unsupported object given to --busco_db, database must be supplied as either a directory or a .tar.gz file!")
+        // Set BUSCO database to empty to allow for --auto-lineage
+        ch_db_for_busco = Channel.of([])
+                            .map{
+                                empty_db ->
+                                    def meta = [:]
+                                    meta['lineage'] = ""
+                                    [ meta, [] ]
+                            }
+                            .collect()
     }
 
     BUSCO (

From b6d3e784f3aea973cecf37c6ea7173c5d2021455 Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 25 Sep 2023 15:16:30 +0000
Subject: [PATCH 08/49] Template update for nf-core/tools version 2.10

---
 .devcontainer/devcontainer.json               |   1 +
 .github/CONTRIBUTING.md                       |   4 +-
 .github/workflows/linting.yml                 |   2 +-
 .github/workflows/release-announcments.yml    |  68 +++++++++
 CHANGELOG.md                                  |   2 +-
 CITATIONS.md                                  |   2 +-
 CODE_OF_CONDUCT.md                            | 133 ++++++++++++++----
 README.md                                     |  21 +--
 assets/multiqc_config.yml                     |   6 +-
 conf/modules.config                           |   9 ++
 docs/output.md                                |   5 +-
 docs/usage.md                                 |  16 ++-
 lib/NfcoreTemplate.groovy                     |  16 +++
 lib/WorkflowMag.groovy                        |   2 +-
 main.nf                                       |   3 +
 modules.json                                  |   6 +-
 .../custom/dumpsoftwareversions/main.nf       |   2 +-
 modules/nf-core/fastqc/main.nf                |   8 +-
 modules/nf-core/multiqc/main.nf               |   2 +-
 nextflow.config                               |   9 +-
 nextflow_schema.json                          |  15 --
 workflows/mag.nf                              |   1 +
 22 files changed, 255 insertions(+), 78 deletions(-)
 create mode 100644 .github/workflows/release-announcments.yml

diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
index ea27a584..4ecfbfe3 100644
--- a/.devcontainer/devcontainer.json
+++ b/.devcontainer/devcontainer.json
@@ -2,6 +2,7 @@
     "name": "nfcore",
     "image": "nfcore/gitpod:latest",
     "remoteUser": "gitpod",
+    "runArgs": ["--privileged"],
 
     // Configure tool-specific properties.
     "customizations": {
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index 2ac5f2d9..eef260f4 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -9,7 +9,9 @@ Please use the pre-filled template to save time.
 However, don't be put off by this template - other more general issues and suggestions are welcome!
 Contributions to the code are even more welcome ;)
 
-> If you need help using or modifying nf-core/mag then the best place to ask is on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::info
+If you need help using or modifying nf-core/mag then the best place to ask is on the nf-core Slack [#mag](https://nfcore.slack.com/channels/mag) channel ([join our Slack here](https://nf-co.re/join/slack)).
+:::
 
 ## Contribution workflow
 
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 888cb4bc..b8bdd214 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -78,7 +78,7 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: "3.8"
+          python-version: "3.11"
           architecture: "x64"
 
       - name: Install dependencies
diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml
new file mode 100644
index 00000000..6ad33927
--- /dev/null
+++ b/.github/workflows/release-announcments.yml
@@ -0,0 +1,68 @@
+name: release-announcements
+# Automatic release toot and tweet anouncements
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+jobs:
+  toot:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: rzr/fediverse-action@master
+        with:
+          access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
+          host: "mstdn.science" # custom host if not "mastodon.social" (default)
+          # GitHub event payload
+          # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
+          message: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+
+  send-tweet:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install dependencies
+        run: pip install tweepy==4.14.0
+      - name: Send tweet
+        shell: python
+        run: |
+          import os
+          import tweepy
+
+          client = tweepy.Client(
+              access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
+              access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
+              consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
+              consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
+          )
+          tweet = os.getenv("TWEET")
+          client.create_tweet(text=tweet)
+        env:
+          TWEET: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+          TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
+          TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
+          TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
+          TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
+
+  bsky-post:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: zentered/bluesky-post-action@v0.0.2
+        with:
+          post: |
+            Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
+
+            Please see the changelog: ${{ github.event.release.html_url }}
+        env:
+          BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
+          BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
+          #
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 3aa0b93d..70b6673d 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## v2.3.1dev - [date]
+## v2.4.0 - [date]
 
 Initial release of nf-core/mag, created with the [nf-core](https://nf-co.re/) template.
 
diff --git a/CITATIONS.md b/CITATIONS.md
index 49d0bcbc..0e8ba8c7 100644
--- a/CITATIONS.md
+++ b/CITATIONS.md
@@ -12,7 +12,7 @@
 
 - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
-  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. Available online https://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
+  > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].
 
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
 
diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md
index f4fd052f..c089ec78 100644
--- a/CODE_OF_CONDUCT.md
+++ b/CODE_OF_CONDUCT.md
@@ -1,18 +1,20 @@
-# Code of Conduct at nf-core (v1.0)
+# Code of Conduct at nf-core (v1.4)
 
 ## Our Pledge
 
-In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of:
+In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of:
 
 - Age
+- Ability
 - Body size
+- Caste
 - Familial status
 - Gender identity and expression
 - Geographical location
 - Level of experience
 - Nationality and national origins
 - Native language
-- Physical and neurological ability
+- Neurodiversity
 - Race or ethnicity
 - Religion
 - Sexual identity and orientation
@@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a
 
 ## Preamble
 
-> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply.
+:::note
+This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply.
+:::
 
-An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva.
+An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about).
+
+Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer.
 
 nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals.
 
-We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc.
+We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc.
 
-Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities.
+Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities.
 
-We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC.
+We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC.
 
-Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re
+Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re.
 
 ## Our Responsibilities
 
-The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
+Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour.
 
-The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
+The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful.
 
-Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC.
+Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC.
 
-## When are where does this Code of Conduct apply?
+## When and where does this Code of Conduct apply?
 
-Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference:
+Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference):
 
 - Communicating with an official project email address.
 - Communicating with community members within the nf-core Slack channel.
 - Participating in hackathons organised by nf-core (both online and in-person events).
-- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence.
-- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc.
+- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace.
+- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc.
 - Representing nf-core on social media. This includes both official and personal accounts.
 
 ## nf-core cares 😊
 
-nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order):
+nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order):
 
 - Ask for consent before sharing another community member’s personal information (including photographs) on social media.
 - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity.
-- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !)
+- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !)
 - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.)
 - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can)
 - Focus on what is best for the team and the community. (When in doubt, ask)
-- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn.
+- Accept feedback, yet be unafraid to question, deliberate, and learn.
 - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!)
-- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**)
+- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**)
 - Take breaks when you feel like you need them.
-- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.)
+- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack)
 
 ## nf-core frowns on 😕
 
-The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces.
+The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces:
 
 - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom.
 - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online.
 - Spamming or trolling of individuals on social media.
-- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention.
-- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience.
+- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention.
+- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience.
 
 ### Online Trolling
 
-The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately.
+The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately.
 
-All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls.
+All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls.
 
-## Procedures for Reporting CoC violations
+## Procedures for reporting CoC violations
 
 If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible.
 
-You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s).
+You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team.
+
+Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course.
+
+All reports will be handled with the utmost discretion and confidentiality.
+
+You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include:
+
+- Your contact information.
+- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct.
+- The behaviour that was in violation and the circumstances surrounding the incident.
+- The approximate time of the behaviour (if different than the time the report was made).
+- Other people involved in the incident, if applicable.
+- If you believe the incident is ongoing.
+- If there is a publicly available record (e.g. mailing list record, a screenshot).
+- Any additional information.
+
+After you file a report, one or more members of our Safety Team will contact you to follow up on your report.
+
+## Who will read and handle reports
+
+All reports will be read and handled by the members of the Safety Team at nf-core.
+
+If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups.
+
+To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with.
+
+## Reviewing reports
+
+After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety.
+
+The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action.
+
+In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information.
 
-Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course.
+Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report.
 
-All reports will be handled with utmost discretion and confidentially.
+## Confidentiality
+
+All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse.
+
+We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved.
+
+## Enforcement
+
+Actions taken by the nf-core’s Safety Team may include, but are not limited to:
+
+- Asking anyone to stop a behaviour.
+- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently.
+- Removing access to the gather.town and Slack, either temporarily or permanently.
+- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons.
+- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident.
+- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently.
+- No action.
 
 ## Attribution and Acknowledgements
 
@@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially.
 
 ## Changelog
 
-### v1.0 - March 12th, 2021
+### v1.4 - February 8th, 2022
+
+- Included a new member of the Safety Team. Corrected a typographical error in the text.
+
+### v1.3 - December 10th, 2021
+
+- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text.
+
+### v1.2 - November 12th, 2021
+
+- Removed information specific to reporting CoC violations at the Hackathon in October 2021.
+
+### v1.1 - October 14th, 2021
+
+- Updated with names of new Safety Officers and specific information for the hackathon in October 2021.
+
+### v1.0 - March 15th, 2021
 
 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC.
diff --git a/README.md b/README.md
index f7a63bd0..c6f2cc49 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,7 @@
 # ![nf-core/mag](docs/images/nf-core-mag_logo_light.png#gh-light-mode-only) ![nf-core/mag](docs/images/nf-core-mag_logo_dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![GitHub Actions CI Status](https://github.com/nf-core/mag/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/mag/actions?query=workflow%3A%22nf-core+CI%22)
+[![GitHub Actions Linting Status](https://github.com/nf-core/mag/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/mag/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mag/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
@@ -29,10 +30,11 @@
 
 ## Usage
 
-> **Note**
-> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
-> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
-> with `-profile test` before running the workflow on actual data.
+:::note
+If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how
+to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline)
+with `-profile test` before running the workflow on actual data.
+:::
 
 <!-- TODO nf-core: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
      Explain what rows and columns represent. For instance (please edit as appropriate):
@@ -61,10 +63,11 @@ nextflow run nf-core/mag \
    --outdir <OUTDIR>
 ```
 
-> **Warning:**
-> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
-> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
-> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::warning
+Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those
+provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;
+see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).
+:::
 
 For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/mag/usage) and the [parameter documentation](https://nf-co.re/mag/parameters).
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index b31b87fc..79ffe5e6 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,9 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/2.3.1dev" target="_blank">nf-core/mag</a>
+  
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/2.4.0" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/2.3.1dev/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/2.4.0/docs/output" target="_blank">documentation</a>.
+  
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000
diff --git a/conf/modules.config b/conf/modules.config
index da58a5d8..39e81386 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -38,4 +38,13 @@ process {
         ]
     }
 
+    withName: 'MULTIQC' {
+        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        publishDir = [
+            path: { "${params.outdir}/multiqc" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
+    }
+
 }
diff --git a/docs/output.md b/docs/output.md
index 9efc681c..fb3133ee 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -35,7 +35,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 
 ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png)
 
-> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::note
+The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality.
+:::
 
 ### MultiQC
 
@@ -62,6 +64,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
   - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
+  - Parameters used by the pipeline run: `params.json`.
 
 </details>
 
diff --git a/docs/usage.md b/docs/usage.md
index d43eb9e2..b32f9587 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -75,7 +75,9 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than
 
 Pipeline settings can be provided in a `yaml` or `json` file via `-params-file <file>`.
 
-> ⚠️ Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::warning
+Do not use `-c <file>` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args).
+:::
 
 The above pipeline run specified with a params file in yaml format:
 
@@ -112,11 +114,15 @@ This version number will be logged in reports when you run the pipeline, so that
 
 To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter.
 
-> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::tip
+If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles.
+:::
 
 ## Core Nextflow arguments
 
-> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::note
+These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen).
+:::
 
 ### `-profile`
 
@@ -124,7 +130,9 @@ Use this parameter to choose a configuration profile. Profiles can give configur
 
 Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below.
 
-> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::info
+We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported.
+:::
 
 The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation).
 
diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy
index 408951ae..01b8653d 100755
--- a/lib/NfcoreTemplate.groovy
+++ b/lib/NfcoreTemplate.groovy
@@ -3,6 +3,7 @@
 //
 
 import org.yaml.snakeyaml.Yaml
+import groovy.json.JsonOutput
 
 class NfcoreTemplate {
 
@@ -222,6 +223,21 @@ class NfcoreTemplate {
         }
     }
 
+    //
+    // Dump pipeline parameters in a json file
+    //
+    public static void dump_parameters(workflow, params) {
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+
+        def timestamp  = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
+        def output_pf  = new File(output_d, "params_${timestamp}.json")
+        def jsonStr    = JsonOutput.toJson(params)
+        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+    }
+
     //
     // Print pipeline summary on completion
     //
diff --git a/lib/WorkflowMag.groovy b/lib/WorkflowMag.groovy
index 53c1e8c9..207d0653 100755
--- a/lib/WorkflowMag.groovy
+++ b/lib/WorkflowMag.groovy
@@ -53,7 +53,7 @@ class WorkflowMag {
 
     public static String toolCitationText(params) {
 
-        // TODO Optionally add in-text citation tools to this list.
+        // TODO nf-core: Optionally add in-text citation tools to this list.
         // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "",
         // Uncomment function in methodsDescriptionText to render in MultiQC report
         def citation_text = [
diff --git a/main.nf b/main.nf
index 33014243..c627b4b3 100644
--- a/main.nf
+++ b/main.nf
@@ -17,6 +17,9 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
+// TODO nf-core: Remove this line if you don't need a FASTA file
+//   This is an example of how to use getGenomeAttribute() to fetch parameters
+//   from igenomes.config using `--genome`
 params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
 
 /*
diff --git a/modules.json b/modules.json
index 168a0265..2525ae08 100644
--- a/modules.json
+++ b/modules.json
@@ -7,17 +7,17 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "f2d63bd5b68925f98f572eed70993d205cc694b7",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
                         "installed_by": ["modules"]
                     }
                 }
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 800a6099..ebc87273 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -5,7 +5,7 @@ process CUSTOM_DUMPSOFTWAREVERSIONS {
     conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index 9ae58381..249f9064 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -5,7 +5,7 @@ process FASTQC {
     conda "bioconda::fastqc=0.11.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
+        'biocontainers/fastqc:0.11.9--0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -29,7 +29,11 @@ process FASTQC {
     printf "%s %s\\n" $rename_to | while read old_name new_name; do
         [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
     done
-    fastqc $args --threads $task.cpus $renamed_files
+
+    fastqc \\
+        $args \\
+        --threads $task.cpus \\
+        $renamed_files
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 4b604749..1fc387be 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -4,7 +4,7 @@ process MULTIQC {
     conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0' }"
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path  multiqc_files, stageAs: "?/*"
diff --git a/nextflow.config b/nextflow.config
index 2435b8e5..277c38ad 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -54,7 +54,7 @@ params {
     // Schema validation default options
     validationFailUnrecognisedParams = false
     validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes'
+    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
     validationShowHiddenParams       = false
     validate_params                  = true
 
@@ -154,6 +154,7 @@ profiles {
     }
     apptainer {
         apptainer.enabled      = true
+        apptainer.autoMounts   = true
         conda.enabled          = false
         docker.enabled         = false
         singularity.enabled    = false
@@ -163,8 +164,8 @@ profiles {
     }
     gitpod {
         executor.name          = 'local'
-        executor.cpus          = 16
-        executor.memory        = 60.GB
+        executor.cpus          = 4
+        executor.memory        = 8.GB
     }
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
@@ -228,7 +229,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.3.1dev'
+    version         = '2.4.0'
     doi             = ''
 }
 
diff --git a/nextflow_schema.json b/nextflow_schema.json
index d84b4d03..68f9485e 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -64,14 +64,6 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
-                "igenomes_base": {
-                    "type": "string",
-                    "format": "directory-path",
-                    "description": "Directory / URL base for iGenomes references.",
-                    "default": "s3://ngi-igenomes/igenomes",
-                    "fa_icon": "fas fa-cloud-download-alt",
-                    "hidden": true
-                },
                 "igenomes_ignore": {
                     "type": "boolean",
                     "description": "Do not load the iGenomes reference config.",
@@ -175,14 +167,12 @@
                     "type": "boolean",
                     "description": "Display help text.",
                     "fa_icon": "fas fa-question-circle",
-                    "default": false,
                     "hidden": true
                 },
                 "version": {
                     "type": "boolean",
                     "description": "Display version and exit.",
                     "fa_icon": "fas fa-question-circle",
-                    "default": false,
                     "hidden": true
                 },
                 "publish_dir_mode": {
@@ -206,7 +196,6 @@
                     "type": "boolean",
                     "description": "Send plain-text email instead of HTML.",
                     "fa_icon": "fas fa-remove-format",
-                    "default": false,
                     "hidden": true
                 },
                 "max_multiqc_email_size": {
@@ -221,7 +210,6 @@
                     "type": "boolean",
                     "description": "Do not use coloured log outputs.",
                     "fa_icon": "fas fa-palette",
-                    "default": false,
                     "hidden": true
                 },
                 "hook_url": {
@@ -260,7 +248,6 @@
                     "type": "boolean",
                     "fa_icon": "far fa-eye-slash",
                     "description": "Show all params when using `--help`",
-                    "default": false,
                     "hidden": true,
                     "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters."
                 },
@@ -268,7 +255,6 @@
                     "type": "boolean",
                     "fa_icon": "far fa-check-circle",
                     "description": "Validation of parameters fails when an unrecognised parameter is found.",
-                    "default": false,
                     "hidden": true,
                     "help_text": "By default, when an unrecognised parameter is found, it returns a warinig."
                 },
@@ -276,7 +262,6 @@
                     "type": "boolean",
                     "fa_icon": "far fa-check-circle",
                     "description": "Validation of parameters in lenient more.",
-                    "default": false,
                     "hidden": true,
                     "help_text": "Allows string values that are parseable as numbers or booleans. For further information see [JSONSchema docs](https://github.com/everit-org/json-schema#lenient-mode)."
                 }
diff --git a/workflows/mag.nf b/workflows/mag.nf
index 08a0778f..5365163e 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -120,6 +120,7 @@ workflow.onComplete {
     if (params.email || params.email_on_fail) {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report)
     }
+    NfcoreTemplate.dump_parameters(workflow, params)
     NfcoreTemplate.summary(workflow, params, log)
     if (params.hook_url) {
         NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)

From b2df8da33946fb448cd59be5b7272ad8e79bd014 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 11:10:13 +0200
Subject: [PATCH 09/49] update changelog

---
 CHANGELOG.md              | 12 +++++++++++-
 assets/multiqc_config.yml |  4 ++--
 nextflow.config           |  2 +-
 3 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 0ca54895..bf107581 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,17 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.4.0 - 2023-09-25
+## 2.4.1dev - unreleased
+
+### `Added`
+
+### `Changed`
+
+### `Fixed`
+
+### `Dependencies`
+
+## 2.4.0 - 2023-09-26
 
 ### `Added`
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 4909cb1a..229dbbd8 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mag/2.4.0" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/dev" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/2.4.0/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/dev/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000
diff --git a/nextflow.config b/nextflow.config
index 0ac8d964..3aa6d87c 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -372,7 +372,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version = '2.4.0'
+    version = '2.4.1dev'
     doi             = '10.1093/nargab/lqac007'
 }
 

From 58c4a38835b69ab70c7e9d9f74361bd42e222bcd Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Tue, 26 Sep 2023 09:27:43 +0000
Subject: [PATCH 10/49] [automated] Fix linting with Prettier

---
 assets/multiqc_config.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 17fc6788..3b08a688 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,9 +1,9 @@
 report_comment: >
-  
+
   This report has been generated by the <a href="https://github.com/nf-core/mag/dev/" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
-  
+
 report_section_order:
   "nf-core-mag-methods-description":
     order: -1000

From e2952b0cc4eaadc432c3c60861f43fb2a0b9f4b0 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 11:31:15 +0200
Subject: [PATCH 11/49] fix dumpsoftwware hash

---
 modules.json | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules.json b/modules.json
index 18abbb94..73a43c4d 100644
--- a/modules.json
+++ b/modules.json
@@ -78,7 +78,7 @@
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4",
                         "installed_by": ["modules"]
                     },
                     "dastool/dastool": {
@@ -98,7 +98,7 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
+                        "git_sha": "9a4517e720bc812e95b56d23d15a1653b6db4f53",
                         "installed_by": ["modules"]
                     },
                     "freebayes": {

From 91744ecc96dd1fd17eb2379af26da702f88b368f Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:07:35 +0200
Subject: [PATCH 12/49] Comments after review

---
 assets/multiqc_config.yml | 2 +-
 conf/modules.config       | 9 ---------
 docs/output.md            | 1 -
 main.nf                   | 2 --
 4 files changed, 1 insertion(+), 13 deletions(-)

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 3b08a688..9d667aa9 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,6 +1,6 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/mag/dev/" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/dev" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
 
diff --git a/conf/modules.config b/conf/modules.config
index 962ec7c9..ce30ec8e 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -483,15 +483,6 @@ process {
         ]
     }
 
-    withName: MULTIQC {
-        ext.args   = ""
-        publishDir = [
-            path: { "${params.outdir}/multiqc" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: PRODIGAL {
         ext.args   = "-p meta"
         publishDir = [
diff --git a/docs/output.md b/docs/output.md
index df3d0d69..c61eb48d 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -742,7 +742,6 @@ Summary tool-specific plots and tables of following tools are currently displaye
 - `pipeline_info/`
   - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
   - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
-  - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
   - Parameters used by the pipeline run: `params.json`.
 
 </details>
diff --git a/main.nf b/main.nf
index 7c726c23..ad557fbb 100644
--- a/main.nf
+++ b/main.nf
@@ -24,8 +24,6 @@ nextflow.enable.dsl = 2
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-=======
-========================================================================================
     VALIDATE & PRINT PARAMETER SUMMARY
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */

From bee474939b164090b31607115ef0a5d22aa04de9 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:08:17 +0200
Subject: [PATCH 13/49] Improve TODO

---
 main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/main.nf b/main.nf
index ad557fbb..71285a74 100644
--- a/main.nf
+++ b/main.nf
@@ -17,7 +17,7 @@ nextflow.enable.dsl = 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
+// TODO nf-core: Remove this line if you don't need a FASTA file [TODO: try and test using for --host_fasta and --host_genome]
 //   This is an example of how to use getGenomeAttribute() to fetch parameters
 //   from igenomes.config using `--genome`
 // params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')

From 3f64e920a9ebbb6ef1fa892d3d8db9a484ec2b5e Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:23:34 +0200
Subject: [PATCH 14/49] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bf107581..7d5f9c41 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- [#511](https://github.com/nf-core/mag/pull/511) Update to nf-core 2.10 `TEMPLATE` (by @jfy133)
+
 ### `Fixed`
 
 ### `Dependencies`

From 0c7c31e90cbb6f09cd3e4674474aa4d9fda046e9 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:32:18 +0200
Subject: [PATCH 15/49] Fix CONCOCT missing in some globs

---
 conf/modules.config | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index ce30ec8e..846aa11b 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -660,6 +660,10 @@ process {
         ext.prefix = { "${meta.assembler}-MaxBin2-${meta.id}" }
     }
 
+    withName: DASTOOL_FASTATOCONTIG2BIN_CONCOCT {
+        ext.prefix = { "${meta.assembler}-CONCOCT-${meta.id}" }
+    }
+
     withName: DASTOOL_FASTATOCONTIG2BIN_TIARA {
         ext.prefix = { "${meta.assembler}-${meta.binner}-${meta.id}" }
     }
@@ -687,7 +691,7 @@ process {
                 path: { "${params.outdir}/GenomeBinning/DASTool/bins" },
                 mode: params.publish_dir_mode,
                 // pattern needs to be updated in case of new binning methods
-                pattern: '*-{MetaBAT2,MaxBin2}Refined-*.fa'
+                pattern: '*-{MetaBAT2,MaxBin2,CONCOCT}Refined-*.fa'
             ]
         ]
     }

From 42d70e64e143cb31ea75cb0c95fa983bda0d22c4 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:33:24 +0200
Subject: [PATCH 16/49] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d5f9c41..81527b35 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#512](https://github.com/nf-core/mag/pull/512) Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
+
 ### `Dependencies`
 
 ## 2.4.0 - 2023-09-26

From 8dfb9070c8ae40d1baa0e7d04f916aa9ad0a5676 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:39:07 +0200
Subject: [PATCH 17/49] Fix directory names of GUNC output to prevent
 overwriting

---
 conf/modules.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index ce30ec8e..f9ccf3ec 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -417,7 +417,7 @@ process {
     // Make sure to keep directory in sync with gunc_qc.nf
     withName: 'GUNC_RUN' {
         publishDir = [
-            path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.id}" },
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/raw/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -426,7 +426,7 @@ process {
     // Make sure to keep directory in sync with gunc_qc.nf
     withName: 'GUNC_MERGECHECKM' {
         publishDir = [
-            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.id}" },
+            path: { "${params.outdir}/GenomeBinning/QC/GUNC/checkmmerged/${meta.assembler}-${meta.binner}-${meta.domain}-${meta.refinement}-${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

From 24fe29ee98c3be9a582ef700128d47e7df674a70 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:40:14 +0200
Subject: [PATCH 18/49] Apply suggestions from code review

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 81527b35..708742c2 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,7 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
-- [#512](https://github.com/nf-core/mag/pull/512) Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
+- [#514](https://github.com/nf-core/mag/pull/514) Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
 
 ### `Dependencies`
 

From a2f6168a3a84afa878f32f21db588b740954f018 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:40:55 +0200
Subject: [PATCH 19/49] Update CHANGELOG

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d5f9c41..194236c9 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#515](https://github.com/nf-core/mag/pull/515) Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
+
 ### `Dependencies`
 
 ## 2.4.0 - 2023-09-26

From 5b4be5d2d9b1528b1c783c30abff7766d2d59257 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 26 Sep 2023 14:43:07 +0200
Subject: [PATCH 20/49] Update OUTPUT docs

---
 docs/output.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/docs/output.md b/docs/output.md
index c61eb48d..90d1d8d6 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -557,13 +557,13 @@ If the parameter `--save_checkm_reference` is set, additionally the used the Che
 <summary>Output files</summary>
 
 - `GenomeBinning/QC/gunc_summary.tsv`
-- `GenomeBinning/QC/gunc_checkm_summary.tsv`
+- `GenomeBinning/QC/gunc_checkm_GUNCmmary.tsv`
 - `[gunc-database].dmnd`
 - `GUNC/`
   - `raw/`
-    - `[assembler]-[binner]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC_checkM.merged.tsv`: Per sample GUNC [output](https://grp-bork.embl-community.io/gunc/output.html) containing with taxonomic and completeness QC statistics.
   - `checkmmerged/`
-    - `[assembler]-[binner]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
+    - `[assembler]-[binner]-[domain]-[refinement]-[sample/group]/GUNC.progenomes_2.1.maxCSS_level.tsv`: Per sample GUNC output merged with output from [CheckM](#checkm)
 
 </details>
 

From 2db25be7aaee07bf18732997525aa445074f1bce Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 27 Sep 2023 16:21:59 +0200
Subject: [PATCH 21/49] Update docs/output.md

---
 docs/output.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index 90d1d8d6..e78d244b 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -557,7 +557,7 @@ If the parameter `--save_checkm_reference` is set, additionally the used the Che
 <summary>Output files</summary>
 
 - `GenomeBinning/QC/gunc_summary.tsv`
-- `GenomeBinning/QC/gunc_checkm_GUNCmmary.tsv`
+- `GenomeBinning/QC/gunc_checkm_summary.tsv`
 - `[gunc-database].dmnd`
 - `GUNC/`
   - `raw/`

From e4860c4a118f48a55c94be4455bf7320c21fba03 Mon Sep 17 00:00:00 2001
From: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:31:27 +0100
Subject: [PATCH 22/49] Update megahit.nf

---
 modules/local/megahit.nf | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/modules/local/megahit.nf b/modules/local/megahit.nf
index 5be5d01a..6f31425c 100644
--- a/modules/local/megahit.nf
+++ b/modules/local/megahit.nf
@@ -21,6 +21,11 @@ process MEGAHIT {
     mem = task.memory.toBytes()
     if ( !params.megahit_fix_cpu_1 || task.cpus == 1 )
         """
+        ## Check if we're in the same work directory as a previous failed MEGAHIT run
+        if [[ -d MEGAHIT ]]; then
+            rm -r MEGAHIT/
+        fi
+
         megahit $args -t "${task.cpus}" -m $mem $input -o MEGAHIT --out-prefix "MEGAHIT-${meta.id}"
 
         gzip -c "MEGAHIT/MEGAHIT-${meta.id}.contigs.fa" > "MEGAHIT/MEGAHIT-${meta.id}.contigs.fa.gz"

From f994012e4f7ae6ce302811ab1a69455152752447 Mon Sep 17 00:00:00 2001
From: Jim Downie <19718667+prototaxites@users.noreply.github.com>
Date: Wed, 27 Sep 2023 15:40:47 +0100
Subject: [PATCH 23/49] Update CHANGELOG.md

---
 CHANGELOG.md | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7d5f9c41..c8112003 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails.
+
 ### `Dependencies`
 
 ## 2.4.0 - 2023-09-26

From 4c064c0ad8d45d2aa87f09a89b8bee11f63b0033 Mon Sep 17 00:00:00 2001
From: Gregory Sprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 28 Sep 2023 13:13:02 -0400
Subject: [PATCH 24/49] update centrifuge_db help text

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 85fce7c1..dcb559be 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -481,7 +481,7 @@
                 "centrifuge_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with centrifuge.",
-                    "help_text": "Local directory containing `*.cf` files or path to download compressed tar archive. E.g. ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz."
+                    "help_text": "Local directory containing `*.cf` files, or a URL or local path to a downloaded compressed tar archive of a Centrifuge database. E.g. ftp://ftp.ccb.jhu.edu/pub/infphilo/centrifuge/data/p_compressed+h+v.tar.gz."
                 },
                 "kraken2_db": {
                     "type": "string",

From 9640d644894454d559140cf8044924f320eeba8d Mon Sep 17 00:00:00 2001
From: Gregory Sprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 28 Sep 2023 13:13:24 -0400
Subject: [PATCH 25/49] update kraken2_db help text

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index dcb559be..57c68304 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -486,7 +486,7 @@
                 "kraken2_db": {
                     "type": "string",
                     "description": "Database for taxonomic binning with kraken2.",
-                    "help_text": "Local directory or compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz."
+                    "help_text": "Path to a local directory, archive file, or a URL to compressed tar archive that contains at least the three files `hash.k2d`, `opts.k2d` and `taxo.k2d`. E.g. ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken_8GB_202003.tgz."
                 },
                 "krona_db": {
                     "type": "string",

From d9e7cc8703a5218e555b8693341629dc4324161a Mon Sep 17 00:00:00 2001
From: Gregory Sprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 28 Sep 2023 13:13:42 -0400
Subject: [PATCH 26/49] update busco_db help text

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 nextflow_schema.json | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow_schema.json b/nextflow_schema.json
index 57c68304..837b4e20 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -759,7 +759,7 @@
                 },
                 "busco_db": {
                     "type": "string",
-                    "description": "Download path for BUSCO lineage dataset or path to local directory containing already downloaded and unpacked lineage datasets.",
+                    "description": "Download URL for BUSCO lineage dataset, or path to a tar.gz archive, or local directory containing already downloaded and unpacked lineage datasets.",
                     "help_text": "E.g. https://busco-data.ezlab.org/v5/data/lineages/bacteria_odb10.2020-03-06.tar.gz or '/path/to/buscodb' (files still need to be unpacked manually). Available databases are listed here: https://busco-data.ezlab.org/v5/data/lineages/."
                 },
                 "busco_auto_lineage_prok": {

From 7f054c6d39a3a64d12e205ff9d7ea6dcad789d7a Mon Sep 17 00:00:00 2001
From: Gregory Sprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 28 Sep 2023 13:14:48 -0400
Subject: [PATCH 27/49] fix grammar error

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 modules/local/kraken2_db_preparation.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/kraken2_db_preparation.nf b/modules/local/kraken2_db_preparation.nf
index 78287f48..f6a259fd 100644
--- a/modules/local/kraken2_db_preparation.nf
+++ b/modules/local/kraken2_db_preparation.nf
@@ -19,7 +19,7 @@ process KRAKEN2_DB_PREPARATION {
             ln -sr ${db} database
         fi
 
-        # Make sure {hash,opts,taxo}.k2d are found in direcotry input
+        # Make sure {hash,opts,taxo}.k2d are found in directory input
         if [[ \$(find database/ -name "*.k2d" | wc -l) -lt 3 ]]; then
             error "ERROR: Kraken2 requires '{hash,opts,taxo}.k2d' files."
         fi

From 48f5bc1a26aacfe7536492a39803a23210179814 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Tue, 3 Oct 2023 20:34:12 +0200
Subject: [PATCH 28/49] Correct globs and put summary in right place for Tiara

---
 CHANGELOG.md        |  1 +
 conf/modules.config | 13 +++----------
 docs/output.md      |  4 ++--
 3 files changed, 6 insertions(+), 12 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index ffb4ae15..fd443cef 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
 - [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
 - [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
+- [#517](https://github.com/nf-core/mag/pull/517) - Fix broken publishing of Tiara output files (fix by @jfy133)
 
 ### `Dependencies`
 
diff --git a/conf/modules.config b/conf/modules.config
index 33a19831..c87d71d9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -698,17 +698,10 @@ process {
 
     withName: TIARA_TIARA {
         publishDir = [
-            [
-                path: { "${params.outdir}/Taxonomy/Tiara" },
+                path: { "${params.outdir}/Taxonomy/Tiara/" },
                 mode: params.publish_dir_mode,
-                pattern: { "${meta.assembler}-${meta.id}.tiara.{txt}" }
-            ],
-            [
-                path: { "${params.outdir}/Taxonomy/Tiara/log" },
-                mode: params.publish_dir_mode,
-                pattern: { "log_${meta.assembler}-${meta.id}.tiara.{txt}" }
+                pattern: "*.txt"
             ]
-        ]
         ext.args = { "--min_len ${params.tiara_min_length} --probabilities" }
         ext.prefix = { "${meta.assembler}-${meta.id}.tiara" }
     }
@@ -720,7 +713,7 @@ process {
 
     withName: TIARA_SUMMARY {
         publishDir = [
-            path: { "${params.outdir}/Taxonomy/" },
+            path: { "${params.outdir}/GenomeBinning/Tiara" },
             mode: params.publish_dir_mode,
             pattern: "tiara_summary.tsv"
         ]
diff --git a/docs/output.md b/docs/output.md
index e78d244b..e5e4e014 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -434,12 +434,12 @@ Tiara is a contig classifier that identifies the domain (prokarya, eukarya) of c
 
 - `Taxonomy/Tiara/`
   - `[assembler]-[sample/group].tiara.txt` - Tiara output classifications (with probabilities) for all contigs within the specified sample/group assembly
-  - `log/log_[assembler]-[sample/group].txt` - log file detailing the parameters used by the Tiara model for contig classification.
+  - `log_[assembler]-[sample/group].txt` - log file detailing the parameters used by the Tiara model for contig classification.
 - `GenomeBinning/tiara_summary.tsv` - Summary of Tiara domain classification for all bins.
 
 </details>
 
-Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas `[assembler]-[sample/group].tiara.txt` provides classifications for each contig.
+Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas the files in `Taxonomy/Tiara` provides classifications for each contig.
 
 ### Bin sequencing depth
 

From e550308596862022b1525878cace1b3d3c350971 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 3 Oct 2023 20:40:39 +0200
Subject: [PATCH 29/49] Update CHANGELOG.md

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index fd443cef..6eb70336 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
 - [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
 - [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
-- [#517](https://github.com/nf-core/mag/pull/517) - Fix broken publishing of Tiara output files (fix by @jfy133)
+- [#517](https://github.com/nf-core/mag/pull/517) - Fix missing Tiara output files (fix by @jfy133)
 
 ### `Dependencies`
 

From 90eb2cc51bbb9965193e8bb13fd7ccff4be43952 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 4 Oct 2023 11:06:12 +0200
Subject: [PATCH 30/49] Update docs/output.md

---
 docs/output.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/output.md b/docs/output.md
index e5e4e014..20cab1da 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -439,7 +439,7 @@ Tiara is a contig classifier that identifies the domain (prokarya, eukarya) of c
 
 </details>
 
-Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas the files in `Taxonomy/Tiara` provides classifications for each contig.
+Typically, you would use `tiara_summary.tsv` as the primary file to see which bins or unbins have been classified to which domains at a glance, whereas the files in `Taxonomy/Tiara` provide classifications for each contig.
 
 ### Bin sequencing depth
 

From 3c1e286da3ca513a3158ee9f96cf6131a90f23de Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 4 Oct 2023 12:04:34 +0200
Subject: [PATCH 31/49] Apply suggestions from code review

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6eb70336..f79e8bc4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
 - [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
 - [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
-- [#517](https://github.com/nf-core/mag/pull/517) - Fix missing Tiara output files (fix by @jfy133)
+- [#520](https://github.com/nf-core/mag/pull/520) - Fix missing Tiara output files (fix by @jfy133)
 
 ### `Dependencies`
 

From e09c6a04f8ff5c41745ae92a5e37633c2a0377ac Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 5 Oct 2023 19:45:48 -0400
Subject: [PATCH 32/49] space needed for when adding to p var

---
 modules/local/busco.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/busco.nf b/modules/local/busco.nf
index ab1c5917..fcd1a6da 100644
--- a/modules/local/busco.nf
+++ b/modules/local/busco.nf
@@ -31,7 +31,7 @@ process BUSCO {
     if ( "${lineage_dataset_provided}" == "Y" ) {
         p = "--lineage_dataset dataset/${db}"
     } else if ( "${lineage_dataset_provided}" == "N" ) {
-        p += "--offline --download_path ${db}"
+        p += " --offline --download_path ${db}"
     } else {
         lineage_dataset_provided = ""
     }

From 1f5d1a7e980afbd0dcaf4847c657691233248b78 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 5 Oct 2023 19:48:02 -0400
Subject: [PATCH 33/49] fix busco directory handling and have consistency on
 channel vars

---
 subworkflows/local/busco_qc.nf | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/subworkflows/local/busco_qc.nf b/subworkflows/local/busco_qc.nf
index 4c00436b..be453a48 100644
--- a/subworkflows/local/busco_qc.nf
+++ b/subworkflows/local/busco_qc.nf
@@ -16,9 +16,7 @@ workflow BUSCO_QC {
     if ( !busco_db.isEmpty() ) {
         if ( busco_db.extension == "gz" ) {
             // Expects to be tar.gz!
-            BUSCO_DB_PREPARATION ( busco_db )
-
-            ch_db_for_busco = BUSCO_DB_PREPARATION.out.db
+            ch_db_for_busco = BUSCO_DB_PREPARATION ( busco_db ).db
                                 .map{
                                     meta, db ->
                                         def meta_new = [:]
@@ -28,12 +26,13 @@ workflow BUSCO_QC {
                                 }
         } else if ( busco_db.isDirectory() ) {
             // Set meta to match expected channel cardinality for BUSCO
-            ch_db_for_busco = busco_db
+            ch_db_for_busco = Channel
+                                .of(busco_db)
                                 .map{
                                     db ->
                                         def meta = [:]
-                                        meta['id'] = db.toString().split('/').last()
-                                        if ("${meta['id'].toString().contains('odb10')}" == true) {
+                                        meta['id'] = db.getBaseName()
+                                        if ( meta['id'].contains('odb10') == true ) {
                                             meta['lineage'] = 'Y'
                                         } else {
                                             meta['lineage'] = 'N'
@@ -44,11 +43,12 @@ workflow BUSCO_QC {
         }
     } else {
         // Set BUSCO database to empty to allow for --auto-lineage
-        ch_db_for_busco = Channel.of([])
+        ch_db_for_busco = Channel
+                            .of([])
                             .map{
                                 empty_db ->
                                     def meta = [:]
-                                    meta['lineage'] = ""
+                                    meta['lineage'] = ''
                                     [ meta, [] ]
                             }
                             .collect()

From 42b914db343b59ed86393e0941074a16103e9f25 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 5 Oct 2023 19:48:47 -0400
Subject: [PATCH 34/49] harshil rule on emit lines

---
 modules/local/centrifuge.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/local/centrifuge.nf b/modules/local/centrifuge.nf
index d06bdf37..1e70896a 100644
--- a/modules/local/centrifuge.nf
+++ b/modules/local/centrifuge.nf
@@ -13,7 +13,7 @@ process CENTRIFUGE {
     output:
     tuple val("centrifuge"), val(meta), path("results.krona"), emit: results_for_krona
     path "report.txt"                                        , emit: report
-    tuple val(meta), path("*kreport.txt")                     , emit: kreport
+    tuple val(meta), path("*kreport.txt")                    , emit: kreport
     path "versions.yml"                                      , emit: versions
 
     script:

From 3521da0f0547802ebfe30d74b42d555a243fb521 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 5 Oct 2023 19:51:21 -0400
Subject: [PATCH 35/49] db_name has to be the same as centrifuge filenames

---
 modules/local/centrifuge_db_preparation.nf | 4 ++--
 workflows/mag.nf                           | 9 +++++++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/modules/local/centrifuge_db_preparation.nf b/modules/local/centrifuge_db_preparation.nf
index b4926aff..bd53f952 100644
--- a/modules/local/centrifuge_db_preparation.nf
+++ b/modules/local/centrifuge_db_preparation.nf
@@ -9,8 +9,8 @@ process CENTRIFUGE_DB_PREPARATION {
     path db
 
     output:
-    tuple val("${db.toString().replace(".tar.gz", "")}"), path("*.cf"), emit: db
-    path "versions.yml"                                               , emit: versions
+    path("*.cf")       , emit: db
+    path "versions.yml", emit: versions
 
     script:
     """
diff --git a/workflows/mag.nf b/workflows/mag.nf
index 061a3734..141396a8 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -456,11 +456,16 @@ workflow MAG {
                                     Taxonomic information
     ================================================================================
     */
-    CENTRIFUGE_DB_PREPARATION ( ch_centrifuge_db_file )
+    ch_db_for_centrifuge = CENTRIFUGE_DB_PREPARATION ( ch_centrifuge_db_file ).db
+                            .map{
+                                db ->
+                                    def db_name = db[0].getBaseName().split('\\.')[0]
+                                    [ db_name, db ]
+                            }
 
     CENTRIFUGE (
         ch_short_reads,
-        CENTRIFUGE_DB_PREPARATION.out.db
+        ch_db_for_centrifuge
     )
     ch_versions = ch_versions.mix(CENTRIFUGE.out.versions.first())
 

From 04ceb8998e0ed64d5a86c8d8b5a8cbdc270a979e Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Thu, 5 Oct 2023 20:01:01 -0400
Subject: [PATCH 36/49] update changelog

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 81c47fdc..d9fb9923 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#481](https://github.com/nf-core/mag/pull/481) - Adds MetaEuk for annotation of eukaryotic MAGs, and MMSeqs2 to enable downloading databases for MetaEuk (by @prototaxites)
 - [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb_db` also now supports directory input of an pre-uncompressed GTDB archive directory (reported by @alneberg, fix by @jfy133)
 - [#494](https://github.com/nf-core/mag/pull/494) - Adds support for saving the BAM files from Bowtie2 mapping of input reads back to assembly (fix by @jfy133)
+- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support direcotry input of a pre-uncompressed database archive directory (by @gregorysprenger).
 
 ### `Changed`
 

From d511ebd67c7101ce59b26a598bec1a1262156c13 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Fri, 6 Oct 2023 14:44:16 +0200
Subject: [PATCH 37/49] Fix `nulls` in bin depths

---
 CHANGELOG.md                     | 1 +
 modules/local/mag_depths_plot.nf | 4 ++--
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f79e8bc4..3d8fc04a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
 - [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
 - [#520](https://github.com/nf-core/mag/pull/520) - Fix missing Tiara output files (fix by @jfy133)
+- [#522](https://github.com/nf-core/mag/pull/522) - Fix 'nulls' in depth plot PNG files (fix by @jfy133)
 
 ### `Dependencies`
 
diff --git a/modules/local/mag_depths_plot.nf b/modules/local/mag_depths_plot.nf
index 150d96fa..5f2f44ea 100644
--- a/modules/local/mag_depths_plot.nf
+++ b/modules/local/mag_depths_plot.nf
@@ -11,14 +11,14 @@ process MAG_DEPTHS_PLOT {
     path(sample_groups)
 
     output:
-    tuple val(meta), path("${meta.assembler}-${meta.domain}-${meta.binner}-${meta.id}-binDepths.heatmap.png"), emit: heatmap
+    tuple val(meta), path("${meta.assembler}-${meta.binner}-${meta.id}-binDepths.heatmap.png"), emit: heatmap
     path "versions.yml"                                                                       , emit: versions
 
     script:
     """
     plot_mag_depths.py --bin_depths ${depths} \
                     --groups ${sample_groups} \
-                    --out "${meta.assembler}-${meta.domain}-${meta.binner}-${meta.id}-binDepths.heatmap.png"
+                    --out "${meta.assembler}-${meta.binner}-${meta.id}-binDepths.heatmap.png"
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 5cb4f41045a96694f8204243212b27908bd9045d Mon Sep 17 00:00:00 2001
From: Gregory Sprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Fri, 6 Oct 2023 09:30:02 -0400
Subject: [PATCH 38/49] fix spelling error

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index d9fb9923..5173b691 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#481](https://github.com/nf-core/mag/pull/481) - Adds MetaEuk for annotation of eukaryotic MAGs, and MMSeqs2 to enable downloading databases for MetaEuk (by @prototaxites)
 - [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb_db` also now supports directory input of an pre-uncompressed GTDB archive directory (reported by @alneberg, fix by @jfy133)
 - [#494](https://github.com/nf-core/mag/pull/494) - Adds support for saving the BAM files from Bowtie2 mapping of input reads back to assembly (fix by @jfy133)
-- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support direcotry input of a pre-uncompressed database archive directory (by @gregorysprenger).
+- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).
 
 ### `Changed`
 

From e4525bc36ebfcf3d06c665932215600e8b359a8b Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Fri, 6 Oct 2023 09:39:23 -0400
Subject: [PATCH 39/49] use file attribute getBaseName

---
 subworkflows/local/gtdbtk.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
index f8020aa3..7586b142 100644
--- a/subworkflows/local/gtdbtk.nf
+++ b/subworkflows/local/gtdbtk.nf
@@ -24,7 +24,7 @@ workflow GTDBTK {
                         def completeness  = -1
                         def contamination = -1
                         def missing, duplicated
-                        if (params.busco_db.toString().contains('odb10')) {
+                        if (params.busco_db.getBaseName().contains('odb10')) {
                             missing    = row.'%Missing (specific)'      // TODO or just take '%Complete'?
                             duplicated = row.'%Complete and duplicated (specific)'
                         } else {

From 0d848190e6fe0ec76e9dadbf58017b00288be098 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Fri, 6 Oct 2023 16:56:08 -0400
Subject: [PATCH 40/49] revert back to only decompressing tar.gz files

---
 modules/local/centrifuge_db_preparation.nf | 13 ++++++-------
 modules/local/kraken2_db_preparation.nf    | 19 ++++---------------
 2 files changed, 10 insertions(+), 22 deletions(-)

diff --git a/modules/local/centrifuge_db_preparation.nf b/modules/local/centrifuge_db_preparation.nf
index bd53f952..91a20ab8 100644
--- a/modules/local/centrifuge_db_preparation.nf
+++ b/modules/local/centrifuge_db_preparation.nf
@@ -9,16 +9,15 @@ process CENTRIFUGE_DB_PREPARATION {
     path db
 
     output:
-    path("*.cf")       , emit: db
-    path "versions.yml", emit: versions
+    path "database/*.cf", emit: db
+    path "versions.yml" , emit: versions
 
     script:
     """
-    if [[ -d ${db} ]]; then
-        ln -srf `find ${db}/ -type f -name "*.cf"` \${PWD}
-    else
-        tar -xf "${db}"
-    fi
+    mkdir db_tmp
+    tar -xf "${db}" -C db_tmp
+    mkdir database
+    mv `find db_tmp/ -name "*.cf"` database/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/local/kraken2_db_preparation.nf b/modules/local/kraken2_db_preparation.nf
index f6a259fd..ebc9f912 100644
--- a/modules/local/kraken2_db_preparation.nf
+++ b/modules/local/kraken2_db_preparation.nf
@@ -14,21 +14,10 @@ process KRAKEN2_DB_PREPARATION {
 
     script:
     """
-    if [[ -d ${db} ]]; then
-        if [[ ${db} != database ]]; then
-            ln -sr ${db} database
-        fi
-
-        # Make sure {hash,opts,taxo}.k2d are found in directory input
-        if [[ \$(find database/ -name "*.k2d" | wc -l) -lt 3 ]]; then
-            error "ERROR: Kraken2 requires '{hash,opts,taxo}.k2d' files."
-        fi
-    else
-        mkdir db_tmp
-        tar -xf "${db}" -C db_tmp
-        mkdir database
-        mv `find db_tmp/ -name "*.k2d"` database/
-    fi
+    mkdir db_tmp
+    tar -xf "${db}" -C db_tmp
+    mkdir database
+    mv `find db_tmp/ -name "*.k2d"` database/
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From 10ae0393b73210fd290d3fcb88f624bef4c803d2 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Fri, 6 Oct 2023 16:57:00 -0400
Subject: [PATCH 41/49] handle centrifuge and kraken db parsing

---
 workflows/mag.nf | 60 ++++++++++++++++++++++++++++++++++++++----------
 1 file changed, 48 insertions(+), 12 deletions(-)

diff --git a/workflows/mag.nf b/workflows/mag.nf
index 141396a8..21cbddb8 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -162,17 +162,15 @@ if (params.gunc_db) {
 }
 
 if(params.centrifuge_db){
-    ch_centrifuge_db_file = Channel
-        .value(file( "${params.centrifuge_db}" ))
+    ch_centrifuge_db_file = file(params.centrifuge_db, checkIfExists: true)
 } else {
-    ch_centrifuge_db_file = Channel.empty()
+    ch_centrifuge_db_file = []
 }
 
 if(params.kraken2_db){
-    ch_kraken2_db_file = Channel
-        .value(file( "${params.kraken2_db}" ))
+    ch_kraken2_db_file = file(params.kraken2_db, checkIfExists: true)
 } else {
-    ch_kraken2_db_file = Channel.empty()
+    ch_kraken2_db_file = []
 }
 
 if(params.cat_db){
@@ -456,12 +454,29 @@ workflow MAG {
                                     Taxonomic information
     ================================================================================
     */
-    ch_db_for_centrifuge = CENTRIFUGE_DB_PREPARATION ( ch_centrifuge_db_file ).db
+    if ( !ch_centrifuge_db_file.isEmpty() ) {
+        if ( ch_centrifuge_db_file.extension == "gz" || ch_centrifuge_db_file.extension == "tgz" ) {
+            // Expects to be tar.gz!
+            ch_db_for_centrifuge = CENTRIFUGE_DB_PREPARATION ( ch_centrifuge_db_file ).db
+        } else if ( ch_centrifuge_db_file.isDirectory() ) {
+            ch_db_for_centrifuge = Channel
+                                    .fromPath( "${ch_centrifuge_db_file}/*.cf" )
+        } else {
+            ch_db_for_centrifuge = Channel.empty()
+        }
+    } else {
+        ch_db_for_centrifuge = Channel.empty()
+    }
+
+    // Centrifuge val(db_name) has to be the basename of any of the
+    //   index files up to but not including the final .1.cf
+    ch_db_for_centrifuge = ch_db_for_centrifuge
+                            .collect()
                             .map{
                                 db ->
                                     def db_name = db[0].getBaseName().split('\\.')[0]
                                     [ db_name, db ]
-                            }
+                            }.view()
 
     CENTRIFUGE (
         ch_short_reads,
@@ -469,12 +484,33 @@ workflow MAG {
     )
     ch_versions = ch_versions.mix(CENTRIFUGE.out.versions.first())
 
-    KRAKEN2_DB_PREPARATION (
-        ch_kraken2_db_file
-    )
+    if ( !ch_kraken2_db_file.isEmpty() ) {
+        if ( ch_kraken2_db_file.extension == "gz" || ch_kraken2_db_file.extension == "tgz" ) {
+            // Expects to be tar.gz!
+            ch_db_for_kraken2 = KRAKEN2_DB_PREPARATION ( ch_kraken2_db_file ).db
+        } else if ( ch_kraken2_db_file.isDirectory() ) {
+            ch_db_for_kraken2 = Channel
+                                    .fromPath( "${ch_kraken2_db_file}/*.k2d" )
+                                    .collect()
+                                    .map{
+                                        file ->
+                                            if (file.size() >= 3) {
+                                                def db_name = file[0].getParent().getName()
+                                                [ db_name, file ]
+                                            } else {
+                                                error("Kraken2 requires '{hash,opts,taxo}.k2d' files.")
+                                            }
+                                    }
+        } else {
+            ch_db_for_kraken2 = Channel.empty()
+        }
+    } else {
+        ch_db_for_kraken2 = Channel.empty()
+    }
+
     KRAKEN2 (
         ch_short_reads,
-        KRAKEN2_DB_PREPARATION.out.db
+        ch_db_for_kraken2
     )
     ch_versions = ch_versions.mix(KRAKEN2.out.versions.first())
 

From e77e44d73c1bc3859bae3d803a3ecc08db5217db Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Sun, 8 Oct 2023 13:30:43 -0400
Subject: [PATCH 42/49] less verbose way of checking multiple file extensions

---
 subworkflows/local/busco_qc.nf | 2 +-
 workflows/mag.nf               | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/subworkflows/local/busco_qc.nf b/subworkflows/local/busco_qc.nf
index be453a48..ce92efd5 100644
--- a/subworkflows/local/busco_qc.nf
+++ b/subworkflows/local/busco_qc.nf
@@ -14,7 +14,7 @@ workflow BUSCO_QC {
 
     main:
     if ( !busco_db.isEmpty() ) {
-        if ( busco_db.extension == "gz" ) {
+        if ( busco_db.extension in ['gz', 'tgz'] ) {
             // Expects to be tar.gz!
             ch_db_for_busco = BUSCO_DB_PREPARATION ( busco_db ).db
                                 .map{
diff --git a/workflows/mag.nf b/workflows/mag.nf
index 21cbddb8..adb8aa00 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -455,7 +455,7 @@ workflow MAG {
     ================================================================================
     */
     if ( !ch_centrifuge_db_file.isEmpty() ) {
-        if ( ch_centrifuge_db_file.extension == "gz" || ch_centrifuge_db_file.extension == "tgz" ) {
+        if ( ch_centrifuge_db_file.extension in ['gz', 'tgz'] ) {
             // Expects to be tar.gz!
             ch_db_for_centrifuge = CENTRIFUGE_DB_PREPARATION ( ch_centrifuge_db_file ).db
         } else if ( ch_centrifuge_db_file.isDirectory() ) {
@@ -485,7 +485,7 @@ workflow MAG {
     ch_versions = ch_versions.mix(CENTRIFUGE.out.versions.first())
 
     if ( !ch_kraken2_db_file.isEmpty() ) {
-        if ( ch_kraken2_db_file.extension == "gz" || ch_kraken2_db_file.extension == "tgz" ) {
+        if ( ch_kraken2_db_file.extension in ['gz', 'tgz'] ) {
             // Expects to be tar.gz!
             ch_db_for_kraken2 = KRAKEN2_DB_PREPARATION ( ch_kraken2_db_file ).db
         } else if ( ch_kraken2_db_file.isDirectory() ) {

From 21fcad26e4ba2176d3a618097451cdf7869a9170 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Sun, 8 Oct 2023 13:31:26 -0400
Subject: [PATCH 43/49] remove view function from channel

---
 workflows/mag.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflows/mag.nf b/workflows/mag.nf
index adb8aa00..788a3b9e 100644
--- a/workflows/mag.nf
+++ b/workflows/mag.nf
@@ -476,7 +476,7 @@ workflow MAG {
                                 db ->
                                     def db_name = db[0].getBaseName().split('\\.')[0]
                                     [ db_name, db ]
-                            }.view()
+                            }
 
     CENTRIFUGE (
         ch_short_reads,

From 55fd64048213b6a00a59e07fb0c63e1fef1e7ad2 Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Sun, 8 Oct 2023 13:40:26 -0400
Subject: [PATCH 44/49] use getSimpleName file attribute

---
 modules/local/busco_db_preparation.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/local/busco_db_preparation.nf b/modules/local/busco_db_preparation.nf
index a56a5af6..bd0c3898 100644
--- a/modules/local/busco_db_preparation.nf
+++ b/modules/local/busco_db_preparation.nf
@@ -10,8 +10,8 @@ process BUSCO_DB_PREPARATION {
     path database
 
     output:
-    tuple val("${database.toString().replace(".tar.gz", "")}"), path("buscodb/*"), emit: db
-    path "versions.yml"                                                         , emit: versions
+    tuple val("${database.getSimpleName()}"), path("buscodb/*"), emit: db
+    path "versions.yml"                                        , emit: versions
 
     script:
     """

From d122b4998010348ed4422da810681b439e42ca2c Mon Sep 17 00:00:00 2001
From: gregorysprenger <42686628+gregorysprenger@users.noreply.github.com>
Date: Sun, 8 Oct 2023 13:42:09 -0400
Subject: [PATCH 45/49] update changelog

---
 CHANGELOG.md | 30 +++++++++++++++++++++++++-----
 1 file changed, 25 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5173b691..e4fcbfe7 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,27 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.4.0 - 2023-09-07
+## 2.4.1dev - unreleased
+
+### `Added`
+
+- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).
+
+### `Changed`
+
+- [#511](https://github.com/nf-core/mag/pull/511) - Update to nf-core 2.10 `TEMPLATE` (by @jfy133)
+
+### `Fixed`
+
+- [#514](https://github.com/nf-core/mag/pull/514) - Fix missing CONCOCT files in downstream output (reported by @maxibor, fix by @jfy133)
+- [#515](https://github.com/nf-core/mag/pull/515) - Fix overwriting of GUNC output directories when running with domain classification (reported by @maxibor, fix by @jfy133)
+- [#516](https://github.com/nf-core/mag/pull/516) - Fix edge-case bug where MEGAHIT re-uses previous work directory on resume and fails (reported by @husensofteng, fix by @prototaxites)
+- [#520](https://github.com/nf-core/mag/pull/520) - Fix missing Tiara output files (fix by @jfy133)
+- [#522](https://github.com/nf-core/mag/pull/522) - Fix 'nulls' in depth plot PNG files (fix by @jfy133)
+
+### `Dependencies`
+
+## 2.4.0 - 2023-09-26
 
 ### `Added`
 
@@ -16,17 +36,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#481](https://github.com/nf-core/mag/pull/481) - Adds MetaEuk for annotation of eukaryotic MAGs, and MMSeqs2 to enable downloading databases for MetaEuk (by @prototaxites)
 - [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb_db` also now supports directory input of an pre-uncompressed GTDB archive directory (reported by @alneberg, fix by @jfy133)
 - [#494](https://github.com/nf-core/mag/pull/494) - Adds support for saving the BAM files from Bowtie2 mapping of input reads back to assembly (fix by @jfy133)
-- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).
 
 ### `Changed`
 
-- [#428](https://github.com/nf-core/mag/pull/428) - Update to nf-core 2.8 `TEMPLATE` (by @jfy133)
+- [#428](https://github.com/nf-core/mag/pull/428) [#467](https://github.com/nf-core/mag/pull/467) - Update to nf-core 2.8, 2.9 `TEMPLATE` (by @jfy133)
 - [#429](https://github.com/nf-core/mag/pull/429) - Replaced hardcoded CheckM database auto-download URL to a parameter (reported by @erikrikarddaniel, fix by @jfy133)
 - [#441](https://github.com/nf-core/mag/pull/441) - Deactivated CONCOCT in AWS 'full test' due to very long runtime (fix by @jfy133).
 - [#442](https://github.com/nf-core/mag/pull/442) - Remove warning when BUSCO finds no genes in bins, as this can be expected in some datasets (reported by @Lumimar, fix by @jfy133).
 - [#444](https://github.com/nf-core/mag/pull/444) - Moved BUSCO bash code to script (by @jfy133)
-- [#428](https://github.com/nf-core/mag/pull/429) - Update to nf-core 2.9 `TEMPLATE` (by @jfy133)
-- [#437](https://github.com/nf-core/mag/pull/429) - `--gtdb` parameter is split into `--skip_gtdbtk` and `--gtdb_db` to allow finer control over GTDB database retrieval (fix by @jfy133)
+- [#477](https://github.com/nf-core/mag/pull/477) - `--gtdb` parameter is split into `--skip_gtdbtk` and `--gtdb_db` to allow finer control over GTDB database retrieval (fix by @jfy133)
 - [#500](https://github.com/nf-core/mag/pull/500) - Temporarily disabled downstream processing of both refined and raw bins due to bug (by @jfy133)
 
 ### `Fixed`
@@ -52,6 +70,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | -------- | ---------------- | ----------- |
 | BCFtools | 1.16             | 1.17        |
 | SAMtools | 1.16.1           | 1.17        |
+| fastp    | 0.23.2           | 0.23.4      |
+| MultiQC  | 1.14             | 1.15        |
 
 ## v2.3.2 - [2023-06-23]
 

From f0e4ce64801dafa3f63f0c65a6e5cf471bcb4cfc Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Mon, 9 Oct 2023 09:37:02 +0200
Subject: [PATCH 46/49] Add depcrecateion and updated changed  entries

---
 CHANGELOG.md | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index e4fcbfe7..7a74bd3a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,11 +7,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
-- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).
+- [#504](https://github.com/nf-core/mag/pull/504) - New parameters `--busco_db`, `--kraken2_db`, and `--centrifuge_db` now support directory input of a pre-uncompressed database archive directory (by @gregorysprenger).
 
 ### `Changed`
 
 - [#511](https://github.com/nf-core/mag/pull/511) - Update to nf-core 2.10 `TEMPLATE` (by @jfy133)
+- [#504](https://github.com/nf-core/mag/pull/504) - `--save_busco_reference` is now replaced by `--save_busco_db`  (by @gregorysprenger).
 
 ### `Fixed`
 
@@ -23,6 +24,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Dependencies`
 
+### `Deprecated`
+
+- [#504](https://github.com/nf-core/mag/pull/504) - `--busco_reference`, `--busco_download_path`, `--save_busco_reference` parameters have been deprecated and replaced with new parameters (by @gregorysprenger).
+
 ## 2.4.0 - 2023-09-26
 
 ### `Added`

From 61902221ad4db248ee064d6bd7127e1d336c09af Mon Sep 17 00:00:00 2001
From: nf-core-bot <core@nf-co.re>
Date: Mon, 9 Oct 2023 07:38:28 +0000
Subject: [PATCH 47/49] [automated] Fix linting with Prettier

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7a74bd3a..32ca969a 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -12,7 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`
 
 - [#511](https://github.com/nf-core/mag/pull/511) - Update to nf-core 2.10 `TEMPLATE` (by @jfy133)
-- [#504](https://github.com/nf-core/mag/pull/504) - `--save_busco_reference` is now replaced by `--save_busco_db`  (by @gregorysprenger).
+- [#504](https://github.com/nf-core/mag/pull/504) - `--save_busco_reference` is now replaced by `--save_busco_db` (by @gregorysprenger).
 
 ### `Fixed`
 

From b3e5eec0784a021da72076e4b8fb5ed8b272b004 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Mon, 9 Oct 2023 11:55:36 +0200
Subject: [PATCH 48/49] Update version for release

---
 CHANGELOG.md                 | 2 +-
 assets/multiqc_config.yml    | 4 ++--
 docs/images/mag_workflow.svg | 2 +-
 nextflow.config              | 2 +-
 4 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 32ca969a..eca1c37f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.4.1dev - unreleased
+## 2.5.0 - [2023-10-11]
 
 ### `Added`
 
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
index 9d667aa9..49878c35 100644
--- a/assets/multiqc_config.yml
+++ b/assets/multiqc_config.yml
@@ -1,8 +1,8 @@
 report_comment: >
 
-  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/dev" target="_blank">nf-core/mag</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mag/releases/tag/2.5.0" target="_blank">nf-core/mag</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/mag/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mag/2.5.0/docs/output" target="_blank">documentation</a>.
 
 report_section_order:
   "nf-core-mag-methods-description":
diff --git a/docs/images/mag_workflow.svg b/docs/images/mag_workflow.svg
index cf9dfc1f..293354db 100644
--- a/docs/images/mag_workflow.svg
+++ b/docs/images/mag_workflow.svg
@@ -2694,7 +2694,7 @@
            id="tspan3824"
            style="font-style:normal;font-variant:normal;font-weight:bold;font-stretch:normal;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro Bold';stroke-width:0.264583"
            x="260.85703"
-           y="65.938919">v2.4.0</tspan></text>
+           y="65.938919">v2.5.0</tspan></text>
       <g
          id="g1307"
          transform="translate(3.3065026,127.42992)">
diff --git a/nextflow.config b/nextflow.config
index 74b1878f..56bc9857 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -372,7 +372,7 @@ manifest {
     description     = """Assembly, binning and annotation of metagenomes"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.4.1dev'
+    version = '2.5.0'
     doi             = '10.1093/nargab/lqac007'
 }
 

From e219e7abc979f0c50b4230c99497a0bc0973c657 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 10 Oct 2023 13:32:49 +0200
Subject: [PATCH 49/49] Update CHANGELOG.md [skip ci]

---
 CHANGELOG.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index eca1c37f..21b03689 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 2.5.0 - [2023-10-11]
+## 2.5.0 - [2023-10-10]
 
 ### `Added`