Cleanup issues before release

nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

https://nf-co.re/sarek

MIT License

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Closed szilvajuhos closed 5 years ago

szilvajuhos commented 5 years ago

[ ] rename wgs_calling_regions_CAW.list for GRCh37
[x] QC processes do launch with '--noReports' (should not)
[ ] add check for misspelled parameteres (i.e. adding '--pom file.vcf' is silently ignored) ... more to come as I am testing

maxulysse commented 5 years ago

--noReports has been replaced by --skip all

maxulysse commented 5 years ago

You could specify which QC tool to skip with this --skip params: (bamQC, BCFtools, FastQC, MultiQC, samtools, vcftools, versions)

maxulysse commented 5 years ago

For the other issues, I think it can all be treated in the current draft PR #19

szilvajuhos commented 5 years ago

moved to #19