Merge branch 'dev' into test_multiple_mods

.github/CONTRIBUTING.md

@@ -27,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from
 
 ## Tests
 
+You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to
+receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir <OUTDIR>`.
+
 When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests.
 Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then.
 

.github/PULL_REQUEST_TEMPLATE.md

@@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/mhcq
 - [ ] If necessary, also make a PR on the nf-core/mhcquant _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository.
 - [ ] Make sure your code lints (`nf-core lint`).
 - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir <OUTDIR>`).
+- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir <OUTDIR>`).
 - [ ] Usage Documentation in `docs/usage.md` is updated.
 - [ ] Output Documentation in `docs/output.md` is updated.
 - [ ] `CHANGELOG.md` is updated.

.github/workflows/ci.yml

@@ -28,7 +28,7 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.github/workflows/fix-linting.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # Use the @nf-core-bot token to check out so we can push later
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -24,7 +24,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier @prettier/plugin-php

.github/workflows/linting.yml

@@ -14,9 +14,9 @@ jobs:
   EditorConfig:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install editorconfig-checker
         run: npm install -g editorconfig-checker
@@ -27,9 +27,9 @@ jobs:
   Prettier:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
-      - uses: actions/setup-node@v3
+      - uses: actions/setup-node@v4
 
       - name: Install Prettier
         run: npm install -g prettier
@@ -40,7 +40,7 @@ jobs:
   PythonBlack:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Check code lints with Black
         uses: psf/black@stable
@@ -71,7 +71,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v1

.gitpod.yml

@@ -4,7 +4,9 @@ tasks:
     command: |
       pre-commit install --install-hooks
       nextflow self-update
-
+  - name: unset JAVA_TOOL_OPTIONS
+    command: |
+      unset JAVA_TOOL_OPTIONS
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack
     - codezombiech.gitignore # Language support for .gitignore files

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).
 
-## v2.6.0dev - nfcore/mhcquant
+## v2.6.0dev - [date]
 
 ### `Added`
 

README.md

@@ -34,9 +34,9 @@ On release, automated continuous integration tests run the pipeline on a full-si
 
 First, prepare a samplesheet with your input data that looks as follows:
 
-`samplesheet.tsv`:
+`samplesheet.tsv`
 
-```tsv
+```tsv title="samplesheet.tsv
 ID	Sample	Condition	ReplicateFileName
 1	msrun	tumor	/path/to/msrun.raw|mzML|d
 ```
@@ -53,8 +53,9 @@ nextflow run nf-core/mhcquant
     --outdir ./results
 ```
 
-> [!NOTE]
-> 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/mhcquant/usage) and the [parameter documentation](https://nf-co.re/mhcquant/parameters).
 

assets/multiqc_config.yml

@@ -3,7 +3,7 @@ custom_logo_url: https://github.com/nf-core/mhcquant
 custom_logo_title: "nf-core/mhcquant"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/releases/tag/dev" target="_blank">nf-core/mhcquant</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/tree/dev" target="_blank">nf-core/mhcquant</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/mhcquant/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "nf-core/mhcquant v${version} - ${runName}",
+            "author_name": "nf-core/mhcquant ${version} - ${runName}",
             "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico",
             "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>",
             "fields": [

conf/modules.config

@@ -35,7 +35,7 @@ process {
     }
 
     withName: 'MULTIQC' {
-        ext.args   = params.multiqc_title ? "--title \"$params.multiqc_title\"" : ''
+        ext.args   = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
         publishDir = [
             path: { "${params.outdir}/multiqc" },
             mode: params.publish_dir_mode,

docs/usage.md

@@ -17,7 +17,7 @@ You will need to create a samplesheet with information about the samples you wou
 The `sample` identifiers have to be the same when you have multiple runs. The `Condition` identifiers can be used to further distinguish the sample groups.
 Below is an example for the same sample sequenced across 3 lanes:
 
-```tsv
+```tsv title="samplesheet.tsv
 ID  Sample  Condition  ReplicateFileName
 1   WT  A /path/to/MS/files/WT_A1.raw
 2   WT  A /path/to/MS/files/WT_A2.raw

lib/NfcoreTemplate.groovy

@@ -4,6 +4,7 @@
 
 import org.yaml.snakeyaml.Yaml
 import groovy.json.JsonOutput
+import nextflow.extension.FilesEx
 
 class NfcoreTemplate {
 
@@ -141,12 +142,14 @@ class NfcoreTemplate {
             try {
                 if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
                 // Try to send HTML e-mail using sendmail
+                def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html")
+                sendmail_tf.withWriter { w -> w << sendmail_html }
                 [ 'sendmail', '-t' ].execute() << sendmail_html
                 log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
             } catch (all) {
                 // Catch failures and try with plaintext
                 def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
-                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
                     mail_cmd += [ '-A', mqc_report ]
                 }
                 mail_cmd.execute() << email_html
@@ -155,14 +158,16 @@ class NfcoreTemplate {
         }
 
         // Write summary e-mail HTML to a file
-        def output_d = new File("${params.outdir}/pipeline_info/")
-        if (!output_d.exists()) {
-            output_d.mkdirs()
-        }
-        def output_hf = new File(output_d, "pipeline_report.html")
+        def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html")
         output_hf.withWriter { w -> w << email_html }
-        def output_tf = new File(output_d, "pipeline_report.txt")
+        FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html");
+        output_hf.delete()
+
+        // Write summary e-mail TXT to a file
+        def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt")
         output_tf.withWriter { w -> w << email_txt }
+        FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt");
+        output_tf.delete()
     }
 
     //
@@ -227,15 +232,14 @@ 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 filename   = "params_${timestamp}.json"
+        def temp_pf    = new File(workflow.launchDir.toString(), ".${filename}")
         def jsonStr    = JsonOutput.toJson(params)
-        output_pf.text = JsonOutput.prettyPrint(jsonStr)
+        temp_pf.text   = JsonOutput.prettyPrint(jsonStr)
+
+        FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json")
+        temp_pf.delete()
     }
 
     //

modules.json

@@ -7,12 +7,12 @@
                 "nf-core": {
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "bba7e362e4afead70653f84d8700588ea28d0f9e",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "4ab13872435962dadc239979554d13709e20bf29",
                         "installed_by": ["modules"]
                     }
                 }

modules/local/openms_cometadapter.nf

@@ -2,10 +2,10 @@ process OPENMS_COMETADAPTER {
     tag "$meta.id"
     label 'process_high'
 
-    conda "bioconda::openms-thirdparty=3.0.0"
+    conda "bioconda::openms-thirdparty=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
-        'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
+        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_3' :
+        'biocontainers/openms-thirdparty:3.1.0--h9ee0642_3' }"
 
     input:
         tuple val(meta), path(mzml), path(fasta)

modules/local/openms_decoydatabase.nf

@@ -2,10 +2,10 @@ process OPENMS_DECOYDATABASE {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
         tuple val(meta), path(fasta)

modules/local/openms_falsediscoveryrate.nf

@@ -2,10 +2,10 @@ process OPENMS_FALSEDISCOVERYRATE  {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
         tuple val(meta), path(idxml)

modules/local/openms_featurefinderidentification.nf

@@ -2,10 +2,10 @@ process OPENMS_FEATUREFINDERIDENTIFICATION  {
     tag "$meta.id"
     label 'process_medium'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
     tuple val(meta), path(mzml), path(id_int), path(id_ext)

modules/local/openms_featurelinkerunlabeledkd.nf

@@ -2,10 +2,10 @@ process OPENMS_FEATURELINKERUNLABELEDKD {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::openms-thirdparty=3.0.0"
+    conda "bioconda::openms-thirdparty=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.0.0--h9ee0642_1' :
-        'biocontainers/openms-thirdparty:3.0.0--h9ee0642_1' }"
+        'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_3' :
+        'biocontainers/openms-thirdparty:3.1.0--h9ee0642_3' }"
 
     input:
         tuple val(meta), path(features)

modules/local/openms_filefilter.nf

@@ -2,10 +2,10 @@ process OPENMS_FILEFILTER {
     tag "$meta.id"
     label 'process_low'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
         tuple val(meta), path(mzml)

modules/local/openms_idconflictresolver.nf

@@ -2,10 +2,10 @@ process OPENMS_IDCONFLICTRESOLVER {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
         tuple val(meta), path(consensus)

modules/local/openms_idfilter.nf

@@ -2,10 +2,10 @@ process OPENMS_IDFILTER {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
         tuple val(meta), path(idxml), val(peptide_filter)

modules/local/openms_idmerger.nf

@@ -2,10 +2,10 @@ process OPENMS_IDMERGER {
     tag "$meta.id"
     label 'process_single'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
         tuple val(meta), path(idxmls)

modules/local/openms_idripper.nf

@@ -2,10 +2,10 @@ process OPENMS_IDRIPPER {
     tag "${meta.id}"
     label 'process_single'
 
-    conda "bioconda::openms=3.0.0"
+    conda "bioconda::openms=3.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/openms:3.0.0--h8964181_1' :
-        'biocontainers/openms:3.0.0--h8964181_1' }"
+        'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' :
+        'biocontainers/openms:3.1.0--h8964181_3' }"
 
     input:
         tuple val(meta), path(merged_idxml)