Merge pull request #548 from nf-core/template-update

Template update v2.14.1
nf-core · May 14, 2024 · 6e59239 · 6e59239
2 parents f93c357 + 9838708
commit 6e59239
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Showing 26 changed files with 265 additions and 224 deletions.
diff --git a/.editorconfig b/.editorconfig
@@ -28,10 +28,6 @@ indent_style = unset
 [/assets/email*]
 indent_size = unset
 
-# ignore Readme
-[README.md]
-indent_style = unset
-
-# ignore python
+# ignore python and markdown
 [*.{py,md}]
 indent_style = unset
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -8,12 +8,12 @@ on:
     types: [published]
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
     if: github.repository == 'nf-core/raredisease'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - name: Launch workflow via Seqera Platform
         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)
@@ -33,7 +33,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
@@ -5,13 +5,13 @@ name: nf-core AWS test
 on:
   workflow_dispatch:
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS tests
     if: github.repository == 'nf-core/raredisease'
     runs-on: ubuntu-latest
     steps:
-      # Launch workflow using Tower CLI tool action
-      - name: Launch workflow via tower
+      # Launch workflow using Seqera Platform CLI tool action
+      - name: Launch workflow via Seqera Platform
         uses: seqeralabs/action-tower-launch@v2
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
@@ -27,7 +27,7 @@ jobs:
 
       - uses: actions/upload-artifact@v4
         with:
-          name: Tower debug log file
+          name: Seqera Platform debug log file
           path: |
-            tower_action_*.log
-            tower_action_*.json
+            seqera_platform_action_*.log
+            seqera_platform_action_*.json
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -31,10 +31,10 @@ jobs:
           - "-profile test_one_sample,docker"
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 

diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -14,6 +14,8 @@ on:
   pull_request:
     types:
       - opened
+      - edited
+      - synchronize
     branches:
       - master
   pull_request_target:
@@ -28,14 +30,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
       - name: Disk space cleanup
         uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
       - uses: eWaterCycle/setup-singularity@931d4e31109e875b13309ae1d07c70ca8fbc8537 # v7
         with:
@@ -68,8 +70,17 @@ jobs:
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
 
-      - name: Run the downloaded pipeline
+      - name: Run the downloaded pipeline (stub)
+        id: stub_run_pipeline
+        continue-on-error: true
         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
+      - name: Run the downloaded pipeline (stub run not supported)
+        id: run_pipeline
+        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        env:
+          NXF_SINGULARITY_CACHEDIR: ./
+          NXF_SINGULARITY_HOME_MOUNT: true
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
diff --git a/.github/workflows/fix-linting.yml b/.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@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
         with:
           token: ${{ secrets.nf_core_bot_auth_token }}
 
@@ -32,9 +32,9 @@ jobs:
           GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }}
 
       # Install and run pre-commit
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -14,13 +14,12 @@ jobs:
   pre-commit:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Set up Python 3.11
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - name: Set up Python 3.12
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: 3.11
-          cache: "pip"
+          python-version: "3.12"
 
       - name: Install pre-commit
         run: pip install pre-commit
@@ -32,14 +31,14 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out pipeline code
-        uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
       - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+        uses: nf-core/setup-nextflow@v2
 
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
           architecture: "x64"
 
       - name: Install dependencies
@@ -60,7 +59,7 @@ jobs:
 
       - name: Upload linting log file artifact
         if: ${{ always() }}
-        uses: actions/upload-artifact@5d5d22a31266ced268874388b861e4b58bb5c2f3 # v4
+        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
           name: linting-logs
           path: |

diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@f6b0bace624032e30a85a8fd9c1a7f8f611f5737 # v3
+        uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
         with:
           workflow: linting.yml
           workflow_conclusion: completed

diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
@@ -12,7 +12,7 @@ jobs:
       - name: get topics and convert to hashtags
         id: get_topics
         run: |
-          curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ' >> $GITHUB_OUTPUT
+          echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')"  >> $GITHUB_OUTPUT
 
       - uses: rzr/fediverse-action@master
         with:
@@ -25,13 +25,13 @@ jobs:
 
             Please see the changelog: ${{ github.event.release.html_url }}
 
-            ${{ steps.get_topics.outputs.GITHUB_OUTPUT }} #nfcore #openscience #nextflow #bioinformatics
+            ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
 
   send-tweet:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
         with:
           python-version: "3.10"
       - name: Install dependencies

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -7,4 +7,6 @@ lint:
     - docs/images/nf-core-raredisease_logo_dark.png
     - docs/images/nf-core-raredisease_logo_light.png
     - assets/nf-core-raredisease_logo_light.png
+  modules_config: False
 repository_type: pipeline
+nf_core_version: "2.14.1"
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,6 +3,9 @@ repos:
     rev: "v3.1.0"
     hooks:
       - id: prettier
+        additional_dependencies:
+          - prettier@3.2.5
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@
 [![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/)
-[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/raredisease)
+[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)
 
 [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
 

diff --git a/conf/base.config b/conf/base.config
@@ -57,7 +57,4 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
 }
diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config
@@ -11,21 +11,6 @@
 ----------------------------------------------------------------------------------------
 */
 
-//
-// General configuration options
-//
-
-process {
-
-    withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            pattern: '*_versions.yml'
-        ]
-    }
-}
-
 //
 // Read QC options
 //

diff --git a/conf/test.config b/conf/test.config
@@ -34,33 +34,33 @@ params {
     skip_peddy             = true
 
     // Input data
-    input          = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_trio.csv'
+    input          = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_trio.csv'
 
     // Genome references
-    fasta                = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta"
-    fai                  = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reference.fasta.fai"
+    fasta                = params.pipelines_testdata_base_path + 'raredisease/reference/reference.fasta'
+    fai                  = params.pipelines_testdata_base_path + 'raredisease/reference/reference.fasta.fai'
     genome               = 'GRCh37'
-    gnomad_af            = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/gnomad_reformated.tab.gz"
-    intervals_wgs        = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target_wgs.interval_list"
-    intervals_y          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/targetY.interval_list"
-    known_dbsnp          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/dbsnp_-138-.vcf.gz"
-    ml_model             = "https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model"
-    mobile_element_references       = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/mobile_element_references.tsv"
-    mobile_element_svdb_annotations = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv"
-    reduced_penetrance   = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/reduced_penetrance.tsv"
-    score_config_mt      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
-    score_config_snv     = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_snv.ini"
-    score_config_sv      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/rank_model_sv.ini"
-    svdb_query_dbs       = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/svdb_querydb_files.csv"
-    target_bed           = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/target.bed"
-    variant_catalog      = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_catalog.json"
-    vcfanno_lua          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_functions.lua"
-    vcfanno_resources    = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_resources.txt"
-    vcfanno_toml         = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vcfanno_config.toml"
-    variant_consequences_snv = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt"
-    variant_consequences_sv  = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/variant_consequences_v2.txt"
-    vep_cache            = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_cache_and_plugins.tar.gz"
-    vep_filters          = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/hgnc.txt"
+    gnomad_af            = params.pipelines_testdata_base_path + 'raredisease/reference/gnomad_reformated.tab.gz'
+    intervals_wgs        = params.pipelines_testdata_base_path + 'raredisease/reference/target_wgs.interval_list'
+    intervals_y          = params.pipelines_testdata_base_path + 'raredisease/reference/targetY.interval_list'
+    known_dbsnp          = params.pipelines_testdata_base_path + 'raredisease/reference/dbsnp_-138-.vcf.gz'
+    ml_model             = 'https://s3.amazonaws.com/sentieon-release/other/SentieonDNAscopeModel1.0.model'
+    mobile_element_references       = params.pipelines_testdata_base_path + 'raredisease/reference/mobile_element_references.tsv'
+    mobile_element_svdb_annotations = params.pipelines_testdata_base_path + 'raredisease/reference/svdb_querydb_files.csv'
+    reduced_penetrance   = params.pipelines_testdata_base_path + 'raredisease/reference/reduced_penetrance.tsv'
+    score_config_mt      = params.pipelines_testdata_base_path + 'raredisease/reference/rank_model_snv.ini'
+    score_config_snv     = params.pipelines_testdata_base_path + 'raredisease/reference/rank_model_snv.ini'
+    score_config_sv      = params.pipelines_testdata_base_path + 'raredisease/reference/rank_model_sv.ini'
+    svdb_query_dbs       = params.pipelines_testdata_base_path + 'raredisease/reference/svdb_querydb_files.csv'
+    target_bed           = params.pipelines_testdata_base_path + 'raredisease/reference/target.bed'
+    variant_catalog      = params.pipelines_testdata_base_path + 'raredisease/reference/variant_catalog.json'
+    vcfanno_lua          = params.pipelines_testdata_base_path + 'raredisease/reference/vcfanno_functions.lua'
+    vcfanno_resources    = params.pipelines_testdata_base_path + 'raredisease/reference/vcfanno_resources.txt'
+    vcfanno_toml         = params.pipelines_testdata_base_path + 'raredisease/reference/vcfanno_config.toml'
+    variant_consequences_snv = params.pipelines_testdata_base_path + 'raredisease/reference/variant_consequences_v2.txt'
+    variant_consequences_sv  = params.pipelines_testdata_base_path + 'raredisease/reference/variant_consequences_v2.txt'
+    vep_cache            = params.pipelines_testdata_base_path + 'raredisease/reference/vep_cache_and_plugins.tar.gz'
+    vep_filters          = params.pipelines_testdata_base_path + 'raredisease/reference/hgnc.txt'
     vep_cache_version    = 107
-    vep_plugin_files     = "https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/vep_files.csv"
+    vep_plugin_files     = params.pipelines_testdata_base_path + 'raredisease/reference/vep_files.csv'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -15,11 +15,11 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input           = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/testdata/samplesheet_full.csv'
-    intervals_wgs   = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/test_full/genome.interval_list'
-    intervals_y     = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/test_full/genomeY.interval_list'
-    target_bed      = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/test_full/target.bed'
-    variant_catalog = 'https://raw.githubusercontent.com/nf-core/test-datasets/raredisease/reference/test_full/variant_catalog_hg38.json'
+    input           = params.pipelines_testdata_base_path + 'raredisease/testdata/samplesheet_full.csv'
+    intervals_wgs   = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/genome.interval_list'
+    intervals_y     = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/genomeY.interval_list'
+    target_bed      = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/target.bed'
+    variant_catalog = params.pipelines_testdata_base_path + 'raredisease/reference/test_full/variant_catalog_hg38.json'
 
     // Genome references
     genome = 'GRCh38'