Merge branch 'TEMPLATE' of https://github.com/nf-core/chipseq into me…

…rging-template-3.0.2

.github/workflows/ci.yml

@@ -11,14 +11,16 @@ on:
 
 env:
   NXF_ANSI_LOG: false
+  NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
+  NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
 
 concurrency:
   group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}"
   cancel-in-progress: true
 
 jobs:
   test:
-    name: Run pipeline with test data
+    name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
     # Only run on push if this is the nf-core dev branch (merged PRs)
     if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/chipseq') }}"
     runs-on: ubuntu-latest
@@ -27,26 +29,54 @@ jobs:
         NXF_VER:
           - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test"
+        isMaster:
+          - ${{ github.base_ref == 'master' }}
+        # Exclude conda and singularity on dev
+        exclude:
+          - isMaster: false
+            profile: "conda"
+          - isMaster: false
+            profile: "singularity"
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
+      - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Disk space cleanup
-        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
 
       - name: Run pipeline with test data (docker)
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
+
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
+        with:
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
 
       - name: Run pipeline with test data (singularity)
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,singularity --outdir ./results
-        if: "${{ github.base_ref == 'master' }}"
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
+
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
       - name: Run pipeline with test data (conda)
         run: |

.github/workflows/template_version_comment.yml

@@ -10,9 +10,11 @@ jobs:
     steps:
       - name: Check out pipeline code
         uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
+        with:
+          ref: ${{ github.event.pull_request.head.sha }}
 
       - name: Read template version from .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: nichmor/minimal-read-yaml@v0.0.2
         id: read_yml
         with:
           config: ${{ github.workspace }}/.nf-core.yml
@@ -24,20 +26,21 @@ jobs:
 
       - name: Check nf-core outdated
         id: nf_core_outdated
-        run: pip list --outdated | grep nf-core
+        run: echo "OUTPUT=$(pip list --outdated | grep nf-core)" >> ${GITHUB_ENV}
 
       - name: Post nf-core template version comment
         uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         if: |
-          ${{ steps.nf_core_outdated.outputs.stdout }} =~ 'nf-core'
+          contains(env.OUTPUT, 'nf-core')
         with:
           repo-token: ${{ secrets.NF_CORE_BOT_AUTH_TOKEN }}
           allow-repeats: false
           message: |
-            ## :warning: Newer version of the nf-core template is available.
-
-            Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
-            Please update your pipeline to the latest version.
-
-            For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
+            > [!WARNING]
+            > Newer version of the nf-core template is available.
+            >
+            > Your pipeline is using an old version of the nf-core template: ${{ steps.read_yml.outputs['nf_core_version'] }}.
+            > Please update your pipeline to the latest version.
+            >
+            > For more documentation on how to update your pipeline, please see the [nf-core documentation](https://github.com/nf-core/tools?tab=readme-ov-file#sync-a-pipeline-with-the-template) and [Synchronisation documentation](https://nf-co.re/docs/contributing/sync).
           #

.gitignore

@@ -6,3 +6,4 @@ results/
 testing/
 testing*
 *.pyc
+null/

.nf-core.yml

@@ -4,7 +4,7 @@ lint:
     - config_defaults:
         - params.bamtools_filter_se_config
         - params.bamtools_filter_pe_config
-nf_core_version: 3.0.1
+nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline
 template:

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).
 
-## [[2.2.0dev] - [date]
+## v2.2.0dev - [date]
 
 ### Enhancements & fixes
 

assets/multiqc_config.yml

@@ -3,66 +3,6 @@ report_comment: >
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://nf-co.re/chipseq/dev/docs/output" target="_blank">documentation</a>.
 
-data_format: "yaml"
-
-export_plots: true
-
-exclude_modules:
-  - "general_stats"
-
-module_order:
-  - fastqc:
-      name: "LIB: FastQC (raw)"
-      info: "This section of the report shows FastQC results before adapter trimming for individual libraries."
-      path_filters:
-        - "./fastqc/*.zip"
-  - cutadapt:
-      name: "LIB: cutadapt (trimmed)"
-      info: "This section of the report shows the length of trimmed reads by cutadapt for individual libraries."
-  - fastqc:
-      name: "LIB: FastQC (trimmed)"
-      info: "This section of the report shows FastQC results after adapter trimming for individual libraries."
-      path_filters:
-        - "./trimgalore/fastqc/*.zip"
-  - samtools:
-      name: "LIB: SAMTools"
-      info: "This section of the report shows SAMTools results for individual libraries."
-      path_filters:
-        - "./alignment/library/*"
-  - samtools:
-      name: "MERGED LIB: SAMTools (unfiltered)"
-      info: "This section of the report shows SAMTools results after merging libraries and before filtering."
-      path_filters:
-        - "./alignment/merged_library/unfiltered/*.mLb.mkD.sorted.bam*"
-  - picard:
-      name: "MERGED LIB: Picard (unfiltered)"
-      info: "This section of the report shows picard results after merging libraries and before filtering."
-      path_filters:
-        - "./alignment/merged_library/unfiltered/picard_metrics/*"
-  - preseq:
-      name: "MERGED LIB: Preseq (unfiltered)"
-      info: "This section of the report shows Preseq results after merging libraries and before filtering."
-  - samtools:
-      name: "MERGED LIB: SAMTools (filtered)"
-      info: "This section of the report shows SAMTools results after merging libraries and after filtering."
-      path_filters:
-        - "./alignment/merged_library/filtered/*.mLb.clN.sorted.bam*"
-  - picard:
-      name: "MERGED LIB: Picard (filtered)"
-      info: "This section of the report shows picard results after merging libraries and after filtering."
-      path_filters:
-        - "./alignment/merged_library/filtered/picard_metrics/*"
-  - deeptools:
-      name: "MERGED LIB: deepTools"
-      anchor: "mlib_deeptools"
-      info: "This section of the report shows ChIP-seq QC plots generated by deepTools."
-  - featureCounts:
-      name: "MERGED LIB: featureCounts"
-      anchor: "mlib_featurecounts"
-      info: "This section of the report shows featureCounts results for the number of reads assigned to merged library consensus peaks."
-      path_filters:
-        - "./macs3/featurecounts/*.summary"
-
 report_section_order:
   peak_count:
     before: mlib_deeptools

modules.json

@@ -93,7 +93,7 @@
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
+                        "git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
                         "installed_by": ["modules"]
                     },
                     "phantompeakqualtools": {
@@ -217,12 +217,12 @@
                     },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "9d05360da397692321d377b6102d2fb22507c6ef",
+                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "772684d9d66f37b650c8ba5146ac1ee3ecba2acb",
+                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {