Closed jfy133 closed 1 month ago
nf-core lint
overall result: Passed :white_check_mark: :warning:Posted for pipeline commit 09ab6aa
+| ✅ 337 tests passed |+
#| ❔ 1 tests were ignored |#
!| ❗ 24 tests had warnings |!
TODO:
check_samplesheet.py
existFor point 2, reallife example from @maxulysse :
"anyOf": [
{
"dependentRequired": ["fastq_1"]
},
{
"dependentRequired": ["bam"]
}
],
https://github.com/nf-core/sarek/pull/1204
But still see caveat from Phil in original suggestion
My checklist: https://hackmd.io/@jfy133/B1L7b3ni6
The test TSV files: nf-validation-samplesheets.zip
Exmaple test command: nextflow ../main.nf -profile apptainer,test --outdir ./results --input samplesheet-nf-validation.tsv --input nf-validation-samplesheets/02-samplesheet_v3_doublesinglestrandednotuniquesampleid.tsv
currently tested columns: reference_name,fasta,fai,dict,mapper_index,circular_target,mitochondrion_header,snpcapture_bed,pileupcaller_bedfile,pileupcaller_snpfile,hapmap_file,pmdtools_masked_fasta,pmdtools_bed_for_masking,sexdeterrmine_snp_bed,bedtools_feature_file,genotyping_reference_ploidy,genotyping_gatk_dbsnp
🤠🤠🤠🤠🤠🤠 following in our Opa @apeltzer 's footsteps
At some point everybody converges 💪😂🤷♂️
closes #1012
PR checklist
scrape_software_versions.py
nf-core lint .
).nextflow run . -profile test,docker
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).