Important! Template update for nf-core/tools v2.13

.editorconfig

@@ -18,7 +18,12 @@ end_of_line = unset
 insert_final_newline = unset
 trim_trailing_whitespace = unset
 indent_style = unset
-indent_size = unset
+[/subworkflows/nf-core/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
 
 [/assets/email*]
 indent_size = unset
@@ -28,5 +33,5 @@ indent_size = unset
 indent_style = unset
 
 # ignore python
-[*.{py}]
+[*.{py,md}]
 indent_style = unset

.github/workflows/awsfulltest.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # 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
@@ -31,7 +31,7 @@ jobs:
             }
           profiles: test_full
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: Tower debug log file
           path: |

.github/workflows/awstest.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       # Launch workflow using Tower CLI tool action
       - name: Launch workflow via tower
-        uses: seqeralabs/action-tower-launch@v2
+        uses: seqeralabs/action-tower-launch@922e5c8d5ac4e918107ec311d2ebbd65e5982b3d # v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -25,7 +25,7 @@ jobs:
             }
           profiles: test
 
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: Tower debug log file
           path: |

.github/workflows/branch.yml

@@ -19,7 +19,7 @@ jobs:
       # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets
       - name: Post PR comment
         if: failure()
-        uses: mshick/add-pr-comment@v2
+        uses: mshick/add-pr-comment@b8f338c590a895d50bcbfa6c5859251edc8952fc # v2
         with:
           message: |
             ## This PR is against the `master` branch :x:

.github/workflows/ci.yml

@@ -28,13 +28,16 @@ jobs:
           - "latest-everything"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Disk space cleanup
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
+
       - name: Run pipeline with test data
         # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters

.github/workflows/clean-up.yml

@@ -10,7 +10,7 @@ jobs:
       issues: write
       pull-requests: write
     steps:
-      - uses: actions/stale@v9
+      - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
         with:
           stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
           stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."

.github/workflows/download_pipeline.yml

@@ -6,6 +6,11 @@ name: Test successful pipeline download with 'nf-core download'
 #  - the head branch of the pull request is updated, i.e. if fixes for a release are pushed last minute to dev.
 on:
   workflow_dispatch:
+    inputs:
+      testbranch:
+        description: "The specific branch you wish to utilize for the test execution of nf-core download."
+        required: true
+        default: "dev"
   pull_request:
     types:
       - opened
@@ -23,13 +28,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
           architecture: "x64"
-      - uses: eWaterCycle/setup-singularity@v7
+      - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
           singularity-version: 3.8.3
 
@@ -42,13 +47,13 @@ jobs:
         run: |
           echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
           echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${GITHUB_REF#refs/heads/}" >> ${GITHUB_ENV}
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
 
       - name: Download the pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./
         run: |
-          nf-core download  ${{ env.REPO_LOWERCASE }} \
+          nf-core download ${{ env.REPO_LOWERCASE }} \
           --revision ${{ env.REPO_BRANCH }} \
           --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
           --compress "none" \
@@ -64,4 +69,4 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results 
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results

.github/workflows/linting.yml

@@ -14,10 +14,10 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Set up Python 3.11
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: 3.11
           cache: "pip"
@@ -32,12 +32,12 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@v4
+        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@b9f764e8ba5c76b712ace14ecbfcef0e40ae2dd8 # v1
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.11"
           architecture: "x64"
@@ -60,7 +60,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@v4
+        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
         with:
           name: linting-logs
           path: |

.github/workflows/linting_comment.yml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@v3
+        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed
@@ -21,7 +21,7 @@ jobs:
         run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
 
       - name: Post PR comment
-        uses: marocchino/sticky-pull-request-comment@v2
+        uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           number: ${{ steps.pr_number.outputs.pr_number }}

.github/workflows/release-announcements.yml

@@ -9,6 +9,11 @@ jobs:
   toot:
     runs-on: ubuntu-latest
     steps:
+      - name: get topics and convert to hashtags
+        id: get_topics
+        run: |
+          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' > $GITHUB_OUTPUT
+
       - uses: rzr/fediverse-action@master
         with:
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
@@ -20,11 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
+            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
         with:
           python-version: "3.10"
       - name: Install dependencies
@@ -56,7 +63,7 @@ jobs:
   bsky-post:
     runs-on: ubuntu-latest
     steps:
-      - uses: zentered/[email protected]
+      - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
         with:
           post: |
             Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!

README.md

@@ -5,8 +5,8 @@
   </picture>
 </h1>
 
-[![GitHub Actions CI Status](https://github.com/nf-core/variantbenchmarking/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions?query=workflow%3A%22nf-core+CI%22)
-[![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/variantbenchmarking/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/variantbenchmarking/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/variantbenchmarking/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/ci.yml)
+[![GitHub Actions Linting Status](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/variantbenchmarking/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/variantbenchmarking/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/)

assets/email_template.html

@@ -4,7 +4,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge">
   <meta name="viewport" content="width=device-width, initial-scale=1">
 
-  <meta name="description" content="nf-core/variantbenchmarking: Nextflow variant benchmarking pipeline">
+  <meta name="description" content="nf-core/variantbenchmarking: Master benchmarking pipeline for Structural Variant callers ">
   <title>nf-core/variantbenchmarking Pipeline Report</title>
 </head>
 <body>

assets/multiqc_config.yml

@@ -11,3 +11,5 @@ report_section_order:
     order: -1002
 
 export_plots: true
+
+disable_version_detection: true

assets/schema_input.json

@@ -1,29 +1,31 @@
 {
-  "$schema": "http://json-schema.org/draft-07/schema",
-  "$id": "https://raw.githubusercontent.com/nf-core/variantbenchmarking/master/assets/schema_input.json",
-  "title": "nf-core/variantbenchmarking pipeline - params.input schema",
-  "description": "Schema for the file provided with params.input",
-  "type": "array",
-  "items": {
-    "type": "object",
-    "properties": {
-      "test_vcf": {
-        "type": "string",
-        "pattern": "",
-        "errorMessage": "Test VCF must be provided, cannot contain spaces and must have extension '.vcf.gz'"
-      },
-      "caller": {
-        "type": "string",
-        "pattern": "^\\S+$",
-        "errorMessage": "Name of the variant caller used to generate test file"
-      },
-      "vartype": {
-        "type": "string",
-        "pattern": "^\\S+$",
-        "errorMessage": "Variant type to benchmark"
-      }
-
-    },
-    "required": ["test_vcf","caller","vartype"]
-  }
+    "$schema": "http://json-schema.org/draft-07/schema",
+    "$id": "https://raw.githubusercontent.com/nf-core/variantbenchmarking/master/assets/schema_input.json",
+    "title": "nf-core/variantbenchmarking pipeline - params.input schema",
+    "description": "Schema for the file provided with params.input",
+    "type": "array",
+    "items": {
+        "type": "object",
+        "properties": {
+            "test_vcf": {
+                "type": "string",
+                "pattern": "\\S+\\.vcf(\\.gz)?$",
+                "format": "file-path",
+                "errorMessage": "Test VCF must be provided, cannot contain spaces and must have extension '.vcf.gz'"
+            },
+            "caller": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Name of the variant caller used to generate test file",
+                "meta": ["id"]
+            },
+            "vartype": {
+                "type": "string",
+                "pattern": "^\\S+$",
+                "errorMessage": "Variant type to benchmark",
+                "meta": ["vartype"]
+            }
+        },
+        "required": ["test_vcf", "caller", "vartype"]
+    }
 }

assets/svync/delly.yaml

@@ -66,4 +66,3 @@ format:
     number: 2
     type: integer
     description: Split-read support for the ref and alt alleles in the order listed
-

assets/svync/gridss.yaml

@@ -62,4 +62,3 @@ format:
     number: 2
     type: integer
     description: Split-read support for the ref and alt alleles in the order listed
-

assets/svync/manta.yaml

@@ -63,4 +63,3 @@ format:
     number: 2
     type: integer
     description: Split-read support for the ref and alt alleles in the order listed
-

assets/svync/smoove.yaml

@@ -58,4 +58,3 @@ format:
     number: 2
     type: integer
     description: Split-read support for the ref and alt alleles in the order listed
-

bin/add_svtype.py

@@ -37,7 +37,7 @@
 for v in in_vcf:
     svlen=(len(v.alts[0])-len(v.ref))
     limit=args.svlength
-    
+
     if (svlen < -1*limit):
         v.info.update({'SVTYPE':"DEL"})
         v.info.update({'SVLEN':svlen})
@@ -50,7 +50,7 @@
         counter=counter+1
     else:
         anno_vcf.write(v)
-        
+
 in_vcf.close()
 anno_vcf.close()
 logger.info('Finished adding SVTYE/SVLEN to VCF: {}'.format(counter))

bin/annotate_repeat_regions.py

@@ -31,7 +31,7 @@ def print_AF(in_vcf,samplerep,repeatmask,segdup):
                 simple_repeat=temp1.iloc[0].period
             else:
                 simple_repeat='None'
-            
+
             temp2=repeatmask[(repeatmask['genoName']== v.chrom) &( (( v.start > repeatmask['genoStart']-1 ) & ( v.start < repeatmask['genoEnd'] +1 ) )| (( v.stop > repeatmask['genoStart'] -1) & ( v.stop < repeatmask['genoEnd'] +1 ))) ]
 
             if len(temp2) > 0:
@@ -40,7 +40,7 @@ def print_AF(in_vcf,samplerep,repeatmask,segdup):
             else:
                 repname='None'
                 repclass='None'
-                
+
             temp3=segdup[(segdup['chrom']== v.chrom) &( (( v.start > segdup['chromStart']-1 ) & ( v.start < segdup['chromEnd'] +1 ) )| (( v.stop > segdup['chromStart'] -1) & ( v.stop < segdup['chromEnd'] +1 ))) ]
             if len(temp3) > 0:
                 segdups=temp3.iloc[0].fracMatch
@@ -53,13 +53,13 @@ def print_AF(in_vcf,samplerep,repeatmask,segdup):
                     print('DEL', v.ref, len(v.alts[0])- len(v.ref) , v.info['AF'][0],simple_repeat,repname, repclass,segdups, file=out_file)
                 else:
                     print('DEL', '...', len(v.alts[0])- len(v.ref) , v.info['AF'][0],simple_repeat,repname, repclass,segdups, file=out_file)
-                    
+
             elif len(v.alts[0]) -  len(v.ref) > 49:
                 if len(v.ref) -  len(v.alts[0]) < 1001:
                     print('INS', v.alts[0],len(v.alts[0]) -  len(v.ref), v.info['AF'][0],simple_repeat,repname, repclass,segdups, file=out_file)
                 else:
                     print('INS', '...',len(v.alts[0]) -  len(v.ref), v.info['AF'][0],simple_repeat,repname, repclass,segdups, file=out_file)
-                    
+
             else:
                 continue