Resolved merge conflicts

Author: Keerthana-Bhaskaran-TG

.github/workflows/awsfulltest.yml

@@ -1,20 +1,40 @@
 name: nf-core AWS full size tests
-# This workflow is triggered on published releases.
+# This workflow is triggered on PRs opened against the master branch.
 # It can be additionally triggered manually with GitHub actions workflow dispatch button.
 # It runs the -profile 'test_full' on AWS batch
 
 on:
-  release:
-    types: [published]
+  pull_request:
+    branches:
+      - master
   workflow_dispatch:
+  pull_request_review:
+    types: [submitted]
+
 jobs:
-  run-tower:
+  run-platform:
     name: Run AWS full tests
-    if: github.repository == 'nf-core/rnasplice'
+    # run only if the PR is approved by at least 2 reviewers and against the master branch or manually triggered
+    if: github.repository == 'nf-core/rnasplice' && github.event.review.state == 'approved' && github.event.pull_request.base.ref == 'master' || github.event_name == 'workflow_dispatch'
     runs-on: ubuntu-latest
     steps:
-      - name: Launch workflow via tower
+      - uses: octokit/request-action@v2.x
+        id: check_approvals
+        with:
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      - id: test_variables
+        if: github.event_name != 'workflow_dispatch'
+        run: |
+          JSON_RESPONSE='${{ steps.check_approvals.outputs.data }}'
+          CURRENT_APPROVALS_COUNT=$(echo $JSON_RESPONSE | jq -c '[.[] | select(.state | contains("APPROVED")) ] | length')
+          test $CURRENT_APPROVALS_COUNT -ge 2 || exit 1 # At least 2 approvals are required
+      - 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)
+        # on the `test_full.config` test runs with only one set of parameters
         with:
           workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }}
           access_token: ${{ secrets.TOWER_ACCESS_TOKEN }}
@@ -27,9 +47,10 @@ jobs:
               "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/rnasplice/results-${{ github.sha }}"
             }
           profiles: test_full
-      - uses: actions/upload-artifact@v3
+
+      - 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

.github/workflows/ci.yml

@@ -7,218 +7,88 @@ on:
   pull_request:
   release:
     types: [published]
+  workflow_dispatch:
 
 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 full 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/rnasplice') }}"
     runs-on: ubuntu-latest
     strategy:
       matrix:
         NXF_VER:
-          - "23.04.0"
+          - "24.04.2"
           - "latest-everything"
+        profile:
+          - "conda"
+          - "docker"
+          - "singularity"
+        test_name:
+          - "test"
+          # - "test_dexseq"
+          # - "test_edger"
+          # - "test_rmats"
+          # - "test_suppa"
+          # - "test_fastq"
+          # - "test_genome_bam"
+          # - "test_transcriptome_bam"
+          # - "test_salmon_results"
+          # - "test_isoformswitchanalyzer"
+        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@v4
+        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - name: Set up Nextflow
+        uses: nf-core/setup-nextflow@v2
         with:
           version: "${{ matrix.NXF_VER }}"
 
-      - name: Run full pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
-
-  test_dexseq:
-    name: Run DEXSeq pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run DEXSeq pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_dexseq,docker --outdir ./results
-
-  test_edger:
-    name: Run edgeR pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run edgeR pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_edger,docker --outdir ./results
-
-  test_rmats:
-    name: Run rMATS pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run rMATS pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_rmats,docker --outdir ./results
-
-  test_suppa:
-    name: Run SUPPA pipeline with test data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
+      - name: Set up Apptainer
+        if: matrix.profile == 'singularity'
+        uses: eWaterCycle/setup-apptainer@main
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run SUPPA pipeline with test data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_suppa,docker --outdir ./results
-
-  test_fastq:
-    name: Run full pipeline with FASTQ data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run full pipeline with FASTQ data
-        run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_fastq,docker --outdir ./results
-
-  test_genome_bam:
-    name: Run full pipeline with genome BAM data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
-
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
-
-      - name: Run full pipeline with genome BAM data
+      - name: Set up Singularity
+        if: matrix.profile == 'singularity'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_genome_bam,docker --outdir ./results
-
-  test_transcriptome_bam:
-    name: Run full pipeline with transcriptome BAM data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
+          mkdir -p $NXF_SINGULARITY_CACHEDIR
+          mkdir -p $NXF_SINGULARITY_LIBRARYDIR
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
+      - name: Set up Miniconda
+        if: matrix.profile == 'conda'
+        uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3
         with:
-          version: "${{ matrix.NXF_VER }}"
+          miniconda-version: "latest"
+          auto-update-conda: true
+          conda-solver: libmamba
+          channels: conda-forge,bioconda
 
-      - name: Run full pipeline with transcriptome BAM data
+      - name: Set up Conda
+        if: matrix.profile == 'conda'
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_transcriptome_bam,docker --outdir ./results
-
-  test_salmon_results:
-    name: Run full pipeline with Salmon results data
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnasplice') }}"
-    runs-on: ubuntu-latest
-    strategy:
-      matrix:
-        NXF_VER:
-          - "23.04.0"
-          - "latest-everything"
-    steps:
-      - name: Check out pipeline code
-        uses: actions/checkout@v3
+          echo $(realpath $CONDA)/condabin >> $GITHUB_PATH
+          echo $(realpath python) >> $GITHUB_PATH
 
-      - name: Install Nextflow
-        uses: nf-core/setup-nextflow@v1
-        with:
-          version: "${{ matrix.NXF_VER }}"
+      - name: Clean up Disk space
+        uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1
 
-      - name: Run full pipeline with Salmon results data
+      - name: "Run pipeline with test data ${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }}"
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_salmon_results,docker --outdir ./results
+          nextflow run ${GITHUB_WORKSPACE} -profile ${{ matrix.test_name }},${{ matrix.profile }} --outdir ./results

.github/workflows/linting.yml

@@ -58,7 +58,15 @@ jobs:
           GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
-        run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
+
+      - name: Run nf-core pipelines lint --release
+        if: ${{ github.base_ref == 'master' }}
+        env:
+          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
+        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md
 
       - name: Run nf-core pipelines lint --release
         if: ${{ github.base_ref == 'master' }}

.nf-core.yml

@@ -1,2 +1,16 @@
+bump_version: null
+lint: null
+nf_core_version: 3.0.2
+org_path: null
 repository_type: pipeline
-nf_core_version: 2.14.1
+template:
+  author: Ben Southgate, James Ashmore
+  description: Alternative splicing analysis using RNA-seq.
+  force: false
+  is_nfcore: true
+  name: rnasplice
+  org: nf-core
+  outdir: .
+  skip_features: null
+  version: 1.0.5
+update: null

CHANGELOG.md

@@ -3,6 +3,13 @@
 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).
 
+## v1.0.5 - 2024-11-03
+
+- Added IsoformSwitchAnalyzeR to pipeline.
+- Updated to migrate from nf-validation to nf-schema.
+- Updated to remove max_memory, max_cpus, max_time and replace with process resourceLimits.
+- Updated for nf-core template version 3.0.2.
+- Updated to remove lib folder and add utils subworkflows.
 ## Dev v1.0.5dev - TBD - TBD
 
 - Add first steps of leafcutter splicing quantification

CITATIONS.md

@@ -81,6 +81,12 @@
 
   > Nowicka M, Robinson MD (2016). “DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics [version 2; referees: 2 approved].” F1000Research, 5(1356). doi: 10.12688/f1000research.8900.2.
 
+- [IsoformSwitchAnalyzeR](https://www.bioconductor.org/packages/release/bioc/html/IsoformSwitchAnalyzeR.html)
+
+  > Vitting-Seerup K, Sandelin A (2017). “The Landscape of Isoform Switches in Human Cancers.” Mol. Cancer Res. doi:10.1158/1541-7786.MCR-16-0459, doi: 10.1158/1541-7786.MCR-16-0459.
+
+  > Vitting-Seerup K, Sandelin A (2019). “IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences.” Bioinformatics. doi:10.1093/bioinformatics/btz247, doi: 10.1093/bioinformatics/btz247.
+
 - [edgeR](https://bioconductor.org/packages/release/bioc/html/edgeR.html)
 
   > Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi: 10.1093/bioinformatics/btp616.