Merge pull request #555 from nf-core/dev

Release 2.1.0
nf-core · May 29, 2024 · c7a6f38 · c7a6f38
2 parents 1489b71 + 4237c6d
commit c7a6f38
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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:
@@ -68,7 +70,9 @@ 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

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:
+          - [email protected]
+
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"
     hooks:

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,59 @@
 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).
 
+## 2.1.0 - Obelix [2024-05-29]
+
+### `Added`
+
+- A new aligner, bwameme [#553](https://github.com/nf-core/raredisease/pull/553)
+- A new parameter `run_mt_for_wes` to turn on mitochondrial analysis for targeted analysis [#552](https://github.com/nf-core/raredisease/pull/552)
+- A new parameter `bwa_as_fallback` to switch aligner to bwa in case bwamem2 fails [#551](https://github.com/nf-core/raredisease/pull/551)
+- A new parameter `skip_me_calling` to skip mobile element calling and the subsequent annotation of them [#556](https://github.com/nf-core/raredisease/pull/556)
+
+### `Changed`
+
+- Changed valid values for sex according to the PED file format [#550](https://github.com/nf-core/raredisease/pull/550)
+- Refactored config files [#538](https://github.com/nf-core/raredisease/pull/538)
+- Refactored mobile element annotation subworkflow files [#538](https://github.com/nf-core/raredisease/pull/538)
+- Refactored to remove "a process is defined more than once" warning [#557](https://github.com/nf-core/raredisease/pull/557)
+- Updated modules [#558](https://github.com/nf-core/raredisease/pull/558)
+
+### `Fixed`
+
+- Include multiallelic indel sites in CADD scoring jobs [#545](https://github.com/nf-core/raredisease/pull/545)
+- Fixed issues with samtools merge not being run on samples sequenced over multiple lanes [#538](https://github.com/nf-core/raredisease/pull/538)
+- Fixed join issues in the mobile element calling subworkflow which occured when mobile_element_references were not provided [#556](https://github.com/nf-core/raredisease/pull/556)
+
+### Parameters
+
+| Old parameter | New parameter   |
+| ------------- | --------------- |
+|               | bwameme         |
+|               | bwa_as_fallback |
+|               | run_mt_for_wes  |
+|               | skip_me_calling |
+
+:::note
+Parameter has been updated if both old and new parameter information is present.
+Parameter has been added if just the new parameter information is present.
+Parameter has been removed if new parameter information isn't present.
+:::
+
+### Module updates
+
+| Tool     | Old version | New version |
+| -------- | ----------- | ----------- |
+| bwa      | 0.7.17      | 0.7.18      |
+| CADD     | 1.6.1       | 1.6.post1   |
+| Sentieon | 202308.01   | 202308.02   |
+| bwameme  |             | 1.0.6       |
+
+:::note
+Version has been updated if both old and new version information is present.
+Version has been added if just the new version information is present.
+Version has been removed if new version information isn't present.
+:::
+
 ## 2.0.1 - Asterix (Patch) [2024-03-25]
 
 ### `Fixed`

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/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -3,9 +3,9 @@ custom_logo_url: https://github.com/nf-core/raredisease/
 custom_logo_title: "nf-core/raredisease"
 
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.0.1" target="_blank">nf-core/raredisease</a>
+  This report has been generated by the <a href="https://github.com/nf-core/raredisease/releases/tag/2.1.0" target="_blank">nf-core/raredisease</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/raredisease/2.0.1/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/raredisease/2.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-raredisease-methods-description":
     order: -1000

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -40,9 +40,9 @@
                 ]
             },
             "sex": {
-                "type": "integer",
+                "type": "string",
                 "meta": ["sex"],
-                "enum": [0, 1, 2],
+                "enum": ["1", "2", "other"],
                 "errorMessage": "Sex must be provided and cannot contain spaces"
             },
             "phenotype": {

diff --git a/conf/base.config b/conf/base.config
@@ -57,7 +57,9 @@ process {
         errorStrategy = 'retry'
         maxRetries    = 2
     }
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
+    withName: 'NFCORE_RAREDISEASE:RAREDISEASE:.*' {
+        publishDir = [
+            enabled: false
+        ]
     }
 }
diff --git a/conf/modules/align.config b/conf/modules/align.config
@@ -12,36 +12,27 @@
 */
 
 process{
-    withName: '.*ALIGN:.*' {
+
+    withName: '.*ALIGN:FASTP' {
+        ext.args = { [
+            params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
+            '--correction',
+            '--overrepresentation_analysis'
+        ].join(' ').trim() }
         publishDir = [
-            enabled: false
+            path: { "${params.outdir}/trimming" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
 
-    if (!params.skip_fastp) {
-        withName: '.*ALIGN:FASTP' {
-            ext.args = { [
-                params.min_trimmed_length ? "--length_required ${params.min_trimmed_length}" : '',
-                '--correction',
-                '--overrepresentation_analysis'
-            ].join(' ').trim() }
-            publishDir = [
-                path: { "${params.outdir}/trimming" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
-    }
-
-    if (params.save_mapped_as_cram) {
-        withName: '.*ALIGN:SAMTOOLS_VIEW' {
-            ext.args   = { '--output-fmt cram --write-index' }
-            ext.prefix = { "${meta.id}_sorted_md" }
-            publishDir = [
-                path: { "${params.outdir}/alignment" },
-                mode: params.publish_dir_mode,
-                saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-            ]
-        }
+    withName: '.*ALIGN:SAMTOOLS_VIEW' {
+        ext.args   = { '--output-fmt cram --write-index' }
+        ext.prefix = { "${meta.id}_sorted_md" }
+        publishDir = [
+            path: { "${params.outdir}/alignment" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 }