Merge pull request #992 from nf-core/dev

Dev -> Master for v3.11.1 release
nf-core · Mar 31, 2023 · 287afcf · 287afcf
2 parents 48fb9b4 + 104ddaf
commit 287afcf
Show file tree

Hide file tree

Showing 9 changed files with 65 additions and 24 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -35,12 +35,17 @@ jobs:
         with:
           version: "${{ matrix.NXF_VER }}"
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -65,7 +70,7 @@ jobs:
 
   star_salmon:
     name: Test STAR Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -87,12 +92,17 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -122,7 +132,7 @@ jobs:
 
   star_rsem:
     name: Test STAR RSEM with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -133,12 +143,17 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -168,7 +183,7 @@ jobs:
 
   hisat2:
     name: Test HISAT2 with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -179,12 +194,17 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'
@@ -214,7 +234,7 @@ jobs:
 
   salmon:
     name: Test Salmon with workflow parameters
-    if: ${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}
+    if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -225,12 +245,17 @@ jobs:
       - name: Check out pipeline code
         uses: actions/checkout@v2
 
+      - name: Hash Github Workspace
+        id: hash_workspace
+        run: |
+          echo "digest=$(echo RNA_3.10.1_${{ github.workspace }} | md5sum | cut -c 1-25)" >> $GITHUB_OUTPUT
+
       - name: Cache test data
         id: cache-testdata
         uses: actions/cache@v3
         with:
           path: test-datasets/
-          key: rnaseq3_10-test-data
+          key: ${{ steps.hash_workspace.outputs.digest }}
 
       - name: Check out test data
         if: steps.cache-testdata.outputs.cache-hit != 'true'

diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml
@@ -17,7 +17,7 @@ on:
           - gcp
 jobs:
   run-full-tests-on-aws:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' }}
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'aws' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -34,15 +34,15 @@ jobs:
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "aligner": "${{ matrix.aligner }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
   run-full-tests-on-gcp:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' }}
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'gcp' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -59,15 +59,15 @@ jobs:
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "aligner": "${{ matrix.aligner }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
           path: tower_action_*.log
   run-full-tests-on-azure:
-    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' }}
+    if: ${{ github.event.inputs.platform == 'all' || github.event.inputs.platform == 'azure' || !github.event.inputs }}
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -84,10 +84,10 @@ jobs:
           parameters: |
             {
                 "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}",
+                "aligner": "${{ matrix.aligner }}",
                 "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-${{ github.sha }}/aligner_${{ matrix.aligner }}",
                 "igenomes_base": "${{ secrets.TOWER_IGENOMES_BASE_AZURE }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml
@@ -30,7 +30,6 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
@@ -51,7 +50,6 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file
@@ -72,7 +70,6 @@ jobs:
             {
                 "outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}"
             }
-          wait: false
       - uses: actions/upload-artifact@v3
         with:
           name: Tower debug log file

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,24 @@
 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).
 
+## [[3.11.1](https://github.com/nf-core/rnaseq/releases/tag/3.11.1)] - 2023-03-31
+
+### Credits
+
+Special thanks to the following for their code contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Rob Syme](https://github.com/robsyme)
+- [suhrig](https://github.com/suhrig)
+
+### Enhancements & fixes
+
+- [[#987](https://github.com/nf-core/rnaseq/pull/987)] - Fix issue with incorrect cacheing of test datasets during CI/CD
+- [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
+- Remove `wait: false` option from Tower Actions which is the default
+- Fix release trigger for full-sized multi-cloud tests
+- Adding `[ci fast]` to commit message now skips all tests except for standard `-profile test` pipeline run
+
 ## [[3.11.0](https://github.com/nf-core/rnaseq/releases/tag/3.11.0)] - 2023-03-30
 
 ### Credits

diff --git a/bin/deseq2_qc.r b/bin/deseq2_qc.r
@@ -77,10 +77,10 @@ decompose       <- n_components!=1 && all(sapply(name_components, length)==n_com
 coldata         <- data.frame(samples.vec, sample=samples.vec, row.names=1)
 if (decompose) {
     groupings        <- as.data.frame(lapply(1:n_components, function(i) sapply(name_components, "[[", i)))
-    names(groupings) <- paste0("Group", 1:n_components)
     n_distinct       <- sapply(groupings, function(grp) length(unique(grp)))
     groupings        <- groupings[n_distinct!=1 & n_distinct!=length(samples.vec)]
     if (ncol(groupings)!=0) {
+        names(groupings) <- paste0("Group", 1:ncol(groupings))
         coldata <- cbind(coldata, groupings)
     } else {
         decompose <- FALSE

diff --git a/modules.json b/modules.json
@@ -211,13 +211,13 @@
                     },
                     "umitools/dedup": {
                         "branch": "master",
-                        "git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
+                        "git_sha": "ffe2f5865f608848e440a52b73c304ea79aaf818",
                         "installed_by": ["bam_dedup_stats_samtools_umitools"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "6d9c7e43404e20a97d2f6f88548456afe78282e6",
-                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
+                        "git_sha": "ffe2f5865f608848e440a52b73c304ea79aaf818",
+                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
                     },
                     "untar": {
                         "branch": "master",

diff --git a/modules/nf-core/umitools/dedup/main.nf b/modules/nf-core/umitools/dedup/main.nf
diff --git a/modules/nf-core/umitools/extract/main.nf b/modules/nf-core/umitools/extract/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -261,7 +261,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '3.11.0'
+    version         = '3.11.1'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }