Expand GTF filtering to remove rows with empty transcript ID when required, fix STAR GTF usage #1981
Workflow file for this run
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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 | |
concurrency: | |
group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
cancel-in-progress: true | |
jobs: | |
test: | |
name: Run pipeline with test data | |
# Only run on push if this is the nf-core dev branch (merged PRs) | |
if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq') }}" | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
NXF_VER: | |
- "23.04.0" | |
- "latest-everything" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v3 | |
- name: Install Nextflow | |
uses: nf-core/setup-nextflow@v1 | |
with: | |
version: "${{ matrix.NXF_VER }}" | |
- name: 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: ${{ steps.hash_workspace.outputs.digest }} | |
- name: Check out test data | |
if: steps.cache-testdata.outputs.cache-hit != 'true' | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: rnaseq3 | |
path: test-datasets/ | |
- name: Replace remote paths in samplesheets | |
run: | | |
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
echo "========== $f ============" | |
cat $f | |
echo "========================================" | |
done; | |
- name: Run pipeline with test data | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
star_salmon: | |
name: Test STAR Salmon with workflow parameters | |
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--skip_qc" | |
- "--skip_trimming" | |
- "--gtf false" | |
- "--star_index false" | |
- "--transcript_fasta false" | |
- "--min_mapped_reads 90" | |
- "--with_umi" | |
- "--with_umi --skip_trimming" | |
- "--remove_ribo_rna --skip_qualimap" | |
- "--bam_csi_index" | |
- "--save_align_intermeds --save_reference" | |
- "--featurecounts_group_type false" | |
- "--trimmer fastp" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Hash Github Workspace | |
id: hash_workspace | |
run: | | |
echo "digest=$(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: ${{ steps.hash_workspace.outputs.digest }} | |
- name: Check out test data | |
if: steps.cache-testdata.outputs.cache-hit != 'true' | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: rnaseq3 | |
path: test-datasets/ | |
- name: Replace remote paths in samplesheets | |
run: | | |
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
echo "========== $f ============" | |
cat $f | |
echo "========================================" | |
done; | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with STAR and various parameters | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_salmon ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
star_rsem: | |
name: Test STAR RSEM with workflow parameters | |
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--skip_qc" | |
- "--rsem_index false" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Hash Github Workspace | |
id: hash_workspace | |
run: | | |
echo "digest=$(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: ${{ steps.hash_workspace.outputs.digest }} | |
- name: Check out test data | |
if: steps.cache-testdata.outputs.cache-hit != 'true' | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: rnaseq3 | |
path: test-datasets/ | |
- name: Replace remote paths in samplesheets | |
run: | | |
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
echo "========== $f ============" | |
cat $f | |
echo "========================================" | |
done; | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with RSEM STAR and various parameters | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner star_rsem ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
hisat2: | |
name: Test HISAT2 with workflow parameters | |
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--skip_qc" | |
- "--hisat2_index false" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Hash Github Workspace | |
id: hash_workspace | |
run: | | |
echo "digest=$(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: ${{ steps.hash_workspace.outputs.digest }} | |
- name: Check out test data | |
if: steps.cache-testdata.outputs.cache-hit != 'true' | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: rnaseq3 | |
path: test-datasets/ | |
- name: Replace remote paths in samplesheets | |
run: | | |
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
echo "========== $f ============" | |
cat $f | |
echo "========================================" | |
done; | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with HISAT2 and various parameters | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker --aligner hisat2 ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ | |
pseudo: | |
name: Test Pseudoaligners with workflow parameters | |
if: ${{ (github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/rnaseq')) && !contains(github.event.head_commit.message, '[ci fast]') }} | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
parameters: | |
- "--pseudo_aligner salmon --skip_qc" | |
- "--pseudo_aligner salmon --skip_alignment --skip_pseudo_alignment" | |
- "--pseudo_aligner salmon --salmon_index false --transcript_fasta false" | |
- "--pseudo_aligner kallisto --skip_qc" | |
- "--pseudo_aligner kallisto --skip_alignment --skip_pseudo_alignment" | |
- "--pseudo_aligner kallisto --kallisto_index false --transcript_fasta false" | |
steps: | |
- name: Check out pipeline code | |
uses: actions/checkout@v2 | |
- name: Hash Github Workspace | |
id: hash_workspace | |
run: | | |
echo "digest=$(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: ${{ steps.hash_workspace.outputs.digest }} | |
- name: Check out test data | |
if: steps.cache-testdata.outputs.cache-hit != 'true' | |
uses: actions/checkout@v3 | |
with: | |
repository: nf-core/test-datasets | |
ref: rnaseq3 | |
path: test-datasets/ | |
- name: Replace remote paths in samplesheets | |
run: | | |
for f in ${{ github.workspace }}/test-datasets/samplesheet/v3.10/*.csv; do | |
sed -i "s=https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/=${{ github.workspace }}/test-datasets/=g" $f | |
echo "========== $f ============" | |
cat $f | |
echo "========================================" | |
done; | |
- name: Install Nextflow | |
run: | | |
wget -qO- get.nextflow.io | bash | |
sudo mv nextflow /usr/local/bin/ | |
- name: Run pipeline with Salmon or Kallisto and various parameters | |
run: | | |
nextflow run ${GITHUB_WORKSPACE} -profile test_cache,docker ${{ matrix.parameters }} --outdir ./results --test_data_base ${{ github.workspace }}/test-datasets/ |