Merge branch 'dev' of github.com:nf-core/eager into dev

Author: jfy133

docs/usage.md

@@ -367,8 +367,8 @@ Note the following important points and limitations for setting up:
   * If you truly want to mix SE data and PE data but using mate-pair info for PE mapping, please run FASTQ preprocessing mapping manually and supply BAM files for downstream processing by nf-core/eager
   * If you _regularly_ want to run the situation above, please leave a feature request on github.
 * DamageProfiler, NuclearContamination, MTtoNucRatio and PreSeq are performed on each unique library separately after deduplication (but prior same-treated library merging).
-* 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.).
-* 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.
+* 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.).
+* 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.
 
 ## Clean up