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Add multisample CI test #44

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5 changes: 4 additions & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
parameters:
- ""
- "--input assets/samplesheet_multisample.csv --split_fastq 250 --parallel_snv 1"
NXF_VER:
- "23.04.0"
- "latest-everything"
Expand All @@ -43,4 +46,4 @@ jobs:
# For example: adding multiple test runs with different parameters
# Remember that you can parallelise this by using strategy.matrix
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results ${{ matrix.parameters }}
3 changes: 3 additions & 0 deletions assets/samplesheet_multisample.csv
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
sample,file,family_id,paternal_id,maternal_id,sex,phenotype
HG002_Revio_A,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM,XXX,YYY,1,1
HG002_Revio_B,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM,XXX,YYY,1,1
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