add nf-test to CI #86
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maxulysse
reviewed
Aug 22, 2024
.github/workflows/ci.yml
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| pull_request: | ||
| release: | ||
| types: [published] | ||
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| env: | ||
| NXF_ANSI_LOG: false | ||
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| NFTEST_VER: "0.8.1" |
maxulysse
reviewed
Aug 22, 2024
tests/main.nf.test
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Comment on lines
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| params { | ||
| max_cpus = 2 | ||
| max_memory = '6.GB' | ||
| max_time = '6.h' | ||
| input = 'https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/sarek_full_test_somatic_v3.4.2/samplesheet_somatic.csv' | ||
| outdir = 'results' | ||
| genome = 'GRCh38' | ||
| analysis = 'somatic' | ||
| sample = "SEQC2" | ||
| method = 'sompy,truvari' | ||
| preprocess = "filter_contigs" | ||
| truth_snv = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/sSNV_truth_set_v1.0.chr21.vcf.gz" | ||
| high_conf_snv = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/high-confidence_sSNV_in_HC_regions_v1.2.chr21.vcf.gz" | ||
| truth_indel = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/sINDEL_truth_set_v1.0.chr21.vcf.gz" | ||
| high_conf_indel = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/high-confidence_sINDEL_in_HC_regions_v1.2.chr21.vcf.gz" | ||
| truth_sv = "https://raw.githubusercontent.com/kubranarci/benchmark_datasets/main/somatic/truth/hg38/13059_2022_2816_MOESM4_ESM.vcf.gz" | ||
| itruth_ignore = true |
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I think you just need outdir as the rest is in your test profile
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Then, I should add config as
config "../conf/test.config"
?
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PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).