Merge remote-tracking branch 'upstream/dev' into dev

.github/CONTRIBUTING.md

@@ -116,4 +116,3 @@ To get started:
 Devcontainer specs:
 
 - [DevContainer config](.devcontainer/devcontainer.json)
-- [Dockerfile](.devcontainer/Dockerfile)

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -42,7 +42,7 @@ body:
     attributes:
       label: System information
       description: |
-        * Nextflow version _(eg. 22.10.1)_
+        * Nextflow version _(eg. 23.04.0)_
         * Hardware _(eg. HPC, Desktop, Cloud)_
         * Executor _(eg. slurm, local, awsbatch)_
         * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter, Charliecloud, or Apptainer)_

.github/workflows/awsfulltest.yml

@@ -14,21 +14,26 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
           parameters: |
             {
+              "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-${{ github.sha }}"
             }
-          profiles: test_full,aws_tower
+          profiles: test_full
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/awstest.yml

@@ -12,18 +12,22 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v1
+        uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
           compute_env: ${{ secrets.TOWER_COMPUTE_ENV }}
+          revision: ${{ github.sha }}
           workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/mhcquant/work-${{ github.sha }}
           parameters: |
             {
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/mhcquant/results-test-${{ github.sha }}"
             }
-          profiles: test,aws_tower
+          profiles: test
+
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
-          path: tower_action_*.log
+          path: |
+            tower_action_*.log
+            tower_action_*.json

.github/workflows/ci.yml

@@ -24,7 +24,7 @@ jobs:
     strategy:
       matrix:
         NXF_VER:
-          - "22.10.1"
+          - "23.04.0"
           - "latest-everything"
     steps:
       - name: Check out pipeline code
@@ -46,28 +46,18 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        # Nextflow versions
-        include:
-          # Test pipeline minimum Nextflow version
-          - NXF_VER: "22.10.1"
-            NXF_EDGE: ""
-          # Test latest edge release of Nextflow
-          - NXF_VER: ""
-            NXF_EDGE: "1"
+        NXF_VER:
+          - "23.04.0"
+          - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       - name: Install Nextflow
-        env:
-          NXF_VER: ${{ matrix.NXF_VER }}
-          # Uncomment only if the edge release is more recent than the latest stable release
-          # See https://github.com/nextflow-io/nextflow/issues/2467
-          # NXF_EDGE: ${{ matrix.NXF_EDGE }}
-        run: |
-          wget -qO- get.nextflow.io | bash
-          sudo mv nextflow /usr/local/bin/
+        uses: nf-core/setup-nextflow@v1
+        with:
+          version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with additional params
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --spectrum_batch_size 2000 --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --predict_class_1 --predict_class_2 --predict_RT --spectrum_batch_size 2000 --use_deeplc --use_ms2pip --outdir ./results

.gitpod.yml

@@ -1,4 +1,9 @@
 image: nfcore/gitpod:latest
+tasks:
+  - name: Update Nextflow and setup pre-commit
+    command: |
+      pre-commit install --install-hooks
+      nextflow self-update
 
 vscode:
   extensions: # based on nf-core.nf-core-extensionpack

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Made file extension check case insensitive
 - Added option to provide a default comet parameters file
 - Optimize resource allocations
+- Template update 2.9. [#274](https://github.com/nf-core/mhcquant/pull/274)
 
 ### `Fixed`
 

CITATIONS.md

@@ -26,9 +26,8 @@
 
   > Röst H, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, Rurik M, Schmitt U, Veit J, Walze M, Wojnar D, Wolski WE, Schilling O, Choudhary JS, Malmström L, Aebersold R, Reinert K, Kohlbacher O. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Methods 13 741–748 (2016). doi: 10.1038/nmeth.3959. PubMed PMID: 27575624
 
-- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
-
 - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/)
+
   > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
 
 ## Software packaging/containerisation tools
@@ -47,5 +46,8 @@
 
 - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
 
+  > Merkel, D. (2014). Docker: lightweight linux containers for consistent development and deployment. Linux Journal, 2014(239), 2. doi: 10.5555/2600239.2600241.
+
 - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+
   > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Leon Bichmann, Marissa Dubbelaar
+Copyright (c) Leon Bichmann, Marissa Dubbelaar, Jonas Scheid, Steffen Lemke
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -2,7 +2,7 @@
 
 [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/mhcquant/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.1569909-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.1569909)
 
-[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/)
+[![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/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
@@ -63,7 +63,7 @@ nextflow run nf-core/mhcquant \
 > 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, please refer to the [usage documentation](https://nf-co.re/mhcquant/usage) and the [parameter documentation](https://nf-co.re/mhcquant/parameters).
+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).
 
 ## Pipeline output
 

assets/methods_description_template.yml

@@ -6,17 +6,18 @@ plot_type: "html"
 ## You inject any metadata in the Nextflow '${workflow}' object
 data: |
   <h4>Methods</h4>
-  <p>Data was processed using nf-core/mhcquant v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>).</p>
+  <p>Data was processed using nf-core/mhcquant v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (<a href="https://doi.org/10.1038/s41587-020-0439-x">Ewels <em>et al.</em>, 2020</a>), utilising reproducible software environments from the Bioconda (<a href="https://doi.org/10.1038/s41592-018-0046-7">Grüning <em>et al.</em>, 2018</a>) and Biocontainers (<a href="https://doi.org/10.1093/bioinformatics/btx192">da Veiga Leprevost <em>et al.</em>, 2017</a>) projects.</p>
   <p>The pipeline was executed with Nextflow v${workflow.nextflow.version} (<a href="https://doi.org/10.1038/nbt.3820">Di Tommaso <em>et al.</em>, 2017</a>) with the following command:</p>
   <pre><code>${workflow.commandLine}</code></pre>
+  <p>${tool_citations}</p>
   <h4>References</h4>
   <ul>
     <li>Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. <a href="https://doi.org/10.1038/nbt.3820">https://doi.org/10.1038/nbt.3820</a></li>
     <li>Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. <a href="https://doi.org/10.1038/s41587-020-0439-x">https://doi.org/10.1038/s41587-020-0439-x</a></li>
     <li>Bichmann, L., Nelde, N., Ghosh, M., Heumos, L., Mohr, C., Peltzer, A., Kuchenbecker L., Sachsenberg, T., Walz, J.S., Stevanović, S., & Kohlbacher, O. (2019). MHCquant: Automated and Reproducible Data Analysis for Immunopeptidomics. Journal of Proteome Research, 18 (11), 3876-3884. <a href="https://doi.org/10.1021/acs.jproteome.9b00313">https://doi.org/10.1021/acs.jproteome.9b00313</a></li>
-    <li>O'Donnell, T.J., Rubinsteyn, A., Bonsack, M., Riemer, A.B., Laserson, U., & Hammerbacher, J. (2018). MHCflurry: Open-Source Class I MHC Binding Affinity Prediction. Cell Systems, 7(1), 129-132.e4. <a href="https://doi.org/10.1016/j.cels.2018.05.014">https://doi.org/10.1016/j.cels.2018.05.014</a></li>    
+    <li>O'Donnell, T.J., Rubinsteyn, A., Bonsack, M., Riemer, A.B., Laserson, U., & Hammerbacher, J. (2018). MHCflurry: Open-Source Class I MHC Binding Affinity Prediction. Cell Systems, 7(1), 129-132.e4. <a href="https://doi.org/10.1016/j.cels.2018.05.014">https://doi.org/10.1016/j.cels.2018.05.014</a></li>
     <li>Shao, X.M., Bhattacharya, R., Huang, J., Sivakumar, A., Tokheim, C., Zheng, L., Hirsch, D., Kaminow, B., Omdahl, A., Bonsack, M., Riemer, A.B., Velculescu, V.E., Anagnostou, V., Pagel, K.A., & Karchin, R. (2018). High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunology Research, 8(3), 396-408. <a href="https://doi.org/10.1158/2326-6066.CIR-19-0464">https://doi.org/10.1158/2326-6066.CIR-19-0464</a></li>
-    <li>Weisser, H., & Choudharay, J.S. (2017). Targeted Feature Detection for Data-Dependent Shotgun Proteomics. Journal of Proteome Research, 16(8), 2964-2974. <a href="https://doi.org/10.1021/acs.jproteome.7b00248">https://doi.org/10.1021/acs.jproteome.7b00248</a></li>    
+    <li>Weisser, H., & Choudharay, J.S. (2017). Targeted Feature Detection for Data-Dependent Shotgun Proteomics. Journal of Proteome Research, 16(8), 2964-2974. <a href="https://doi.org/10.1021/acs.jproteome.7b00248">https://doi.org/10.1021/acs.jproteome.7b00248</a></li>
     <li>Schubert, B., Walzer, M., Brachvogel, H-P., Szolek, A., Mohr, C., & Kohlbacher, O. (2016). FRED 2: an immunoinformatics framework for Python. Bioinformatics, 32(13), 2044-6. <a href="https://doi.org/10.1093/bioinformatics/btw113">https://doi.org/10.1093/bioinformatics/btw113</a></li>
     <li>Eng, J.K., Hoopmann, M.R., Jahan, T.A., Egertson, J.D., Noble, W.S., & MacCoss, M.J. (2015). A Deeper Look into Comet—Implementation and Features. Journal of the American Society for Mass Spectrometry, 26(11), 1865-74. <a href="https://doi.org/10.1007/s13361-015-1179-x">https://doi.org/10.1007/s13361-015-1179-x</a></li>
     <li>Weisser, H., Nahnsen, S., Grossmann, J., Nilse, L., Quandt, A., Brauer, H., Sturm, M., Kenar, E., Kohlbacher, O., Aebersold, R., & Malmström, L. (2013). An Automated Pipeline for High-Throughput Label-Free Quantitative Proteomics. Journal of Proteome Research, 12(4), 1628-44. <a href="https://doi.org/10.1021/pr300992u">https://doi.org/10.1021/pr300992u</a></li>

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/mhcquant" target="_blank">nf-core/mhcquant</a>
+  This report has been generated by the <a href="https://github.com/nf-core/mhcquant/2.4.2dev" 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" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/mhcquant/2.4.2dev/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-mhcquant-methods-description":
     order: -1000

assets/schema_input.json

@@ -23,15 +23,19 @@
             },
             "ReplicateFileName": {
                 "type": "string",
-                "errorMessage": "MS file spaces and must have extension '.raw' or '.mzml'",
+                "errorMessage": "MS file spaces and must have extension '.raw'|'.RAW', '.mzml'|'mzML', or '.d'",
                 "anyOf": [
                     {
                         "type": "string",
-                        "pattern": "^\\S+-?\\.raw$"
+                        "pattern": "^(?i)\\S+-?\\.raw$"
                     },
                     {
                         "type": "string",
-                        "pattern": "^\\S+-?\\.mzml$"
+                        "pattern": "^(?i)\\S+-?\\.mzML$"
+                    },
+                    {
+                        "type": "string",
+                        "pattern": "^\\S+-?\\.d$"
                     }
                 ]
             }

assets/slackreport.json

@@ -3,7 +3,7 @@
         {
             "fallback": "Plain-text summary of the attachment.",
             "color": "<% if (success) { %>good<% } else { %>danger<%} %>",
-            "author_name": "sanger-tol/readmapping v${version} - ${runName}",
+            "author_name": "nf-core/mhcquant v${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

@@ -16,7 +16,6 @@ process {
             path: {"${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}"},
             mode: params.publish_dir_mode,
             saveAs: {filename -> filename.equals('versions.yml') ? null : filename},
-            enabled: false
         ]
 
     withName: 'SAMPLESHEET_CHECK' {

conf/test_full.config

@@ -10,8 +10,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-cleanup = true
-
 params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'

docs/usage.md

@@ -62,7 +62,7 @@ An [example samplesheet](../assets/samplesheet.tsv) has been provided with the p
 The typical command for running the pipeline is as follows:
 
 ```console
-nextflow run nf-core/mhcquant --input 'samples.tsv' --outdir <OUTDIR> --fasta 'SWISSPROT_2020.fasta' --allele_sheet 'alleles.tsv' --vcf_sheet 'variants.tsv' --include_proteins_from_vcf --predict_class_1 --spectrum_batch_size 500 -profile docker
+nextflow run nf-core/mhcquant --input 'samples.tsv' --outdir <OUTDIR> --fasta 'SWISSPROT_2020.fasta' --allele_sheet 'alleles.tsv' -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -81,7 +81,8 @@ 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).
-> The above pipeline run specified with a params file in yaml format:
+
+The above pipeline run specified with a params file in yaml format:
 
 ```bash
 nextflow run nf-core/mhcquant -profile docker -params-file params.yaml
@@ -93,7 +94,6 @@ with `params.yaml` containing:
 input: './samplesheet.csv'
 outdir: './results/'
 genome: 'GRCh37'
-input: 'data'
 <...>
 ```