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This is a suggestion to clarify the description of the
--skip_qc
argument. Based on my understanding of the workflow, this argument applies to the stage 4 (post-processing) and 5 (final QC) including DeSeq based QC. I hope this is correct.Clarification of which QCs are skipped is necessary because steps in stage could also be considered as QC steps. Perhaps a list of skipped QCs would be helpful. For example, I am not sure if
--skip_qc
skipsRSeQC
or not.I hope the documentation for this argument could be more informative.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).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).