Merge pull request #991 from drpatelh/actions

drpatelh · web-flow · commit 104ddaf6ef3d · 2023-03-31T15:26:26.000+01:00
Fix Actions to trigger full-sized tests on release
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -70,7 +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:
@@ -132,7 +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:
@@ -183,7 +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:
@@ -234,7 +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:
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
@@ -37,8 +55,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [[#961](https://github.com/nf-core/rnaseq/issues/961)] - Add warnings to STDOUT for all skipped and failed strandedness check samples
 - [[#975](https://github.com/nf-core/rnaseq/issues/975)] - `SALMON_INDEX` runs when using `--aligner star_rsem` even if samples have explicit strandedness
 - Remove HISAT2 from automated AWS full-sized tests
-- [[#988](https://github.com/nf-core/rnaseq/issues/988)] - `DESEQ2_QC_STAR_SALMON` fails when sample names have many components
-- [[#987](https://github.com/nf-core/rnaseq/pull/987)] - Fix issue with incorrect cacheing of test datasets during CI/CD
 
 ### Parameters
 
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'
 }
 

Original file line number	Diff line number	Diff line change
`@@ -30,7 +30,6 @@ jobs:`
`30`	`30`	`{`
`31`	`31`	`"outdir": "${{ secrets.TOWER_BUCKET_AWS }}/rnaseq/results-test-${{ github.sha }}"`
`32`	`32`	`}`
`33`		`- wait: false`
`34`	`33`	`- uses: actions/upload-artifact@v3`
`35`	`34`	`with:`
`36`	`35`	`name: Tower debug log file`
`@@ -51,7 +50,6 @@ jobs:`
`51`	`50`	`{`
`52`	`51`	`"outdir": "${{ secrets.TOWER_BUCKET_GCP }}/rnaseq/results-test-${{ github.sha }}"`
`53`	`52`	`}`
`54`		`- wait: false`
`55`	`53`	`- uses: actions/upload-artifact@v3`
`56`	`54`	`with:`
`57`	`55`	`name: Tower debug log file`
`@@ -72,7 +70,6 @@ jobs:`
`72`	`70`	`{`
`73`	`71`	`"outdir": "${{ secrets.TOWER_BUCKET_AZURE }}/rnaseq/results-test-${{ github.sha }}"`
`74`	`72`	`}`
`75`		`- wait: false`
`76`	`73`	`- uses: actions/upload-artifact@v3`
`77`	`74`	`with:`
`78`	`75`	`name: Tower debug log file`
Original file line number	Diff line number	Diff line change
`@@ -261,7 +261,7 @@ manifest {`
`261`	`261`	`description = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""`
`262`	`262`	`mainScript = 'main.nf'`
`263`	`263`	`nextflowVersion = '!>=22.10.1'`
`264`		`- version = '3.11.0'`
	`264`	`+ version = '3.11.1'`
`265`	`265`	`doi = 'https://doi.org/10.5281/zenodo.1400710'`
`266`	`266`	`}`
`267`	`267`