Merge branch 'dev' into improve_rseqc_strandedness

.github/workflows/ci.yml

@@ -1,12 +1,7 @@
 name: nf-core CI
 # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors
 on:
-  push:
-    branches:
-      - dev
   pull_request:
-  release:
-    types: [published]
 
 env:
   NXF_ANSI_LOG: false
@@ -23,34 +18,23 @@ jobs:
     name: Check for changes
     runs-on: ubuntu-latest
     outputs:
-      nf_test_files: ${{ steps.list.outputs.nf_test_files }}
+      nf_test_files: ${{ steps.list.outputs.components }}
     steps:
-      - uses: actions/setup-python@v4
-        with:
-          python-version: "3.11"
-          architecture: "x64"
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v3
         with:
           fetch-depth: 0
 
-      - name: Install Python dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install gitpython pyyaml
-
-      - name: list nf_test_files
+      - name: List nf-test files
         id: list
+        uses: adamrtalbot/[email protected]
+        with:
+          head: ${{ github.sha }}
+          base: origin/${{ github.base_ref }}
+          include: .github/include.yaml
+
+      - name: print list of nf-test files
         run: |
-          echo nf_test_files=$(python \
-            .github/python/find_changed_files.py \
-            -t pipeline workflow process \
-            --head_ref ${{ github.sha }} \
-            --base_ref origin/${{ github.base_ref }} \
-          ) >> $GITHUB_OUTPUT
-
-      - name: debug
-        run: |
-          echo ${{ steps.list.outputs.nf_test_files }}
+          echo ${{ steps.list.outputs.components }}
 
   test:
     name: ${{ matrix.nf_test_files }} ${{ matrix.profile }} NF-${{ matrix.NXF_VER }}

CHANGELOG.md

@@ -71,11 +71,13 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
 - [PR #1297](https://github.com/nf-core/rnaseq/pull/1297) - Important! Template update for nf-core/tools v2.14.1
 - [PR #1302](https://github.com/nf-core/rnaseq/pull/1302) - Add missing files from Tximport processing
 - [PR #1304](https://github.com/nf-core/rnaseq/pull/1304) - Remove redundant gene TPM outputs
+- [PR #1307](https://github.com/nf-core/rnaseq/pull/1307) - Clarify infer strandedness step in subway map and text
 - [PR #1317](https://github.com/nf-core/rnaseq/pull/1317) - Strip problematic ifEmpty()
 - [PR #1319](https://github.com/nf-core/rnaseq/pull/1319) - Reinstate oncomplete error messages
 - [PR #1310](https://github.com/nf-core/rnaseq/pull/1310) - Reinstate pseudoalignment subworkflow config
 - [PR #1309](https://github.com/nf-core/rnaseq/pull/1309) - Document FASTP sampling
 - [PR #1312](https://github.com/nf-core/rnaseq/pull/1312) - Fix issues with unzipping of GTF/ GFF files without absolute paths
+- [PR #1322](https://github.com/nf-core/rnaseq/pull/1322) - Use pre-built Github Action to detect nf-test changes
 - [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison
 
 ### Parameters

README.md

@@ -23,7 +23,7 @@
 ![nf-core/rnaseq metro map](docs/images/nf-core-rnaseq_metro_map_grey.png)
 
 1. Merge re-sequenced FastQ files ([`cat`](http://www.linfo.org/cat.html))
-2. Sub-sample FastQ files and auto-infer strandedness ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))
+2. Auto-infer strandedness by subsampling and pseudoalignment ([`fq`](https://github.com/stjude-rust-labs/fq), [`Salmon`](https://combine-lab.github.io/salmon/))
 3. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
 4. UMI extraction ([`UMI-tools`](https://github.com/CGATOxford/UMI-tools))
 5. Adapter and quality trimming ([`Trim Galore!`](https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/))