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Co-authored-by: Daniel Straub <42973691+d4straub@users.noreply.github.com>
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@@ -368,7 +368,7 @@ Note the following important points and limitations for setting up:
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* If you _regularly_ want to run the situation above, please leave a feature request on github.
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* DamageProfiler, NuclearContamination, MTtoNucRatio and PreSeq are performed on each unique library separately after deduplication (but prior same-treated library merging).
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* nf-core/eager functionality such as `--run_trim_bam` will be applied to only non-UDG (UDG_Treatment: none) or half-UDG (UDG_Treatment: half) libraries. - Qualimap is run on each sample, after merging of libraries (i.e. your values will reflect the values of all libraries combined - after being damage trimmed etc.).
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* Genotyping will be typically performed on each `sample` independently, as normally all libraries will have been merged together. However, if you have a mixture of single-stranded and double-stranded libraries, you will normally need to genotype separately. In this case you **must** give each the SS and DS libraries _distinct_ `Sample_IDs`; otherwise you will receive a `file collision` error in steps such as `sexdeterrmine`, and then you will need to merge these yourself. We will consider changing this behaviour in the future if there is enough interest.
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* Genotyping will be typically performed on each `sample` independently, as normally all libraries will have been merged together. However, if you have a mixture of single-stranded and double-stranded libraries, you will normally need to genotype separately. In this case you **must** give each the SS and DS libraries _distinct_ `Sample_IDs`; otherwise you will receive a `file collision` error in steps such as `sexdeterrmine`, and then you will need to merge these yourself. We will consider changing this behaviour in the future if there is enough interest.
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## Clean up
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