Added ancient_dna test and reproducibility for binning

conf/base.config

@@ -154,7 +154,7 @@ process {
     }
     //returns exit code 247 when running out of memory
     withName: BOWTIE2_ASSEMBLY_ALIGN {
-        cpus          = { check_max (2    * task.attempt, 'cpus'   ) }
+        cpus          = { check_bowtie2_cpus (8, 'cpus'   ) }
         memory        = { check_max (8.GB * task.attempt, 'memory' ) }
         time          = { check_max (8.h  * task.attempt, 'time'   ) }
         errorStrategy = { task.exitStatus in [143,137,104,134,139,247] ? 'retry' : 'finish' }

conf/test_ancient_dna.config

@@ -15,27 +15,31 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function for ancient DNA step'
 
     // Limit resources so that this can run on GitHub Actions
-    max_cpus   = 2
-    max_memory = '6.GB'
+    //max_cpus   = 2
+    //max_memory = '6.GB'
     max_time   = '6.h'
 
     // Input data
-    input                                = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv'
-    centrifuge_db                        = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_cf.tar.gz"
-    kraken2_db                           = "https://raw.githubusercontent.com/nf-core/test-datasets/mag/test_data/minigut_kraken.tgz"
-    skip_krona                           = true
-    min_length_unbinned_contigs          = 1
-    max_unbinned_contigs                 = 2
-    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'
-    skip_spades                          = false
-    skip_spadeshybrid                    = true
-    bcftools_view_high_variant_quality   = 0
-    bcftools_view_medium_variant_quality = 0
-    bcftools_view_minimal_allelesupport  = 3
-    refine_bins_dastool                  = true
-    refine_bins_dastool_threshold        = 0
-    skip_concoct                         = true
+    input                       = 'https://raw.githubusercontent.com/nf-core/test-datasets/mag/samplesheets/samplesheet.csv'
+    skip_clipping               = true
+    keep_phix                   = true
+    kraken2_db                  = null
+    centrifuge_db               = null
+    skip_krona                  = true
+    megahit_fix_cpu_1           = true
+    skip_spades                 = false
+    spades_fix_cpus             = 1
+    skip_spadeshybrid           = true
+    ancient_dna                 = true
+    skip_quast                  = true
+    skip_prodigal               = true
+    bowtie2_fix_cpu_1           = true
+    binning_map_mode            = 'own'
+    metabat2_fix_cpu_1          = true
+    maxbin2_fix_cpu_1           = true
+    concoct_fix_cpu_1           = true
+    skip_binqc                  = true
+    skip_gtdbtk                 = true
+    skip_prokka                 = true
+    skip_metaeuk                = true
 }

nextflow.config

@@ -141,6 +141,9 @@ params {
     metabat_rng_seed                     = 1
     bowtie2_seed                         = 1
     bowtie2_fix_cpu_1                    = false
+    metabat2_fix_cpu_1                   = false
+    maxbin2_fix_cpu_1                    = false
+    concoct_fix_cpu_1                    = false
 
     // Annotation options
     skip_metaeuk                         = false
@@ -428,3 +431,15 @@ def check_spadeshybrid_cpus (x, attempt ) {
     if (params.spadeshybrid_fix_cpus != -1) return check_max (params.spadeshybrid_fix_cpus, 'cpus' )
     else return check_max (x * attempt, 'cpus' )
 }
+def check_metabat2_cpus (x, attempt ) {
+    if (params.metabat2_fix_cpu_1) return 1
+    else return check_max (x * attempt, 'cpus' )
+}
+def check_maxbin2_cpus (x, attempt ) {
+    if (params.maxbin2_fix_cpu_1) return 1
+    else return check_max (x * attempt, 'cpus' )
+}
+def check_concoct_cpus (x, attempt ) {
+    if (params.concoct_fix_cpu_1) return 1
+    else return check_max (x * attempt, 'cpus' )
+}

workflows/mag/tests/tags.yml

@@ -1,5 +1,7 @@
 test_adapterremoval:
   - ./**
+test_ancient_dna:
+  - ./**
 test_bbnorm:
   - ./**
 test_host_rm:

workflows/mag/tests/test_ancient_dna.nf.test

@@ -0,0 +1,34 @@
+nextflow_workflow {
+
+    name "Test workflow: MAG"
+    script "../main.nf"
+    workflow "MAG"
+    tag "workflows"
+    tag "mag"
+    tag "mag_test_ancient_dna"
+
+    test("Parameters: ancient_dna = true") {
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(
+                    workflow.out.
+                    short_reads,
+                    //workflow.out.assemblies,
+                    //workflow.out.prodigal,
+                    //workflow.out.genomad,
+                    //workflow.out.busco,
+                    //workflow.out.checkm,
+                    //workflow.out.gunc,
+                    //workflow.out.quast_bins,
+                    //workflow.out.cat,
+                    //workflow.out.gtdbtk,
+                    //workflow.out.prokka,
+                    //workflow.out.metaeuk,
+                    //workflow.out.versions
+                ).match()}
+            )
+        }
+    }
+}

workflows/mag/tests/test_ancient_dna.nf.test.snap

@@ -0,0 +1,31 @@
+{
+    "Parameters: ancient_dna = true": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test_minigut",
+                        "group": "0",
+                        "single_end": false
+                    },
+                    [
+                        "/nf-core/test-datasets/raw/mag/test_data/test_minigut_R1.fastq.gz",
+                        "/nf-core/test-datasets/raw/mag/test_data/test_minigut_R2.fastq.gz"
+                    ]
+                ],
+                [
+                    {
+                        "id": "test_minigut_sample2",
+                        "group": "0",
+                        "single_end": false
+                    },
+                    [
+                        "/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R1.fastq.gz",
+                        "/nf-core/test-datasets/raw/mag/test_data/test_minigut_sample2_R2.fastq.gz"
+                    ]
+                ]
+            ]
+        ],
+        "timestamp": "2023-12-15T13:36:01.487711685"
+    }
+}