Add bismark --ignore and --ignore_3prime options #311
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helenxl
changed the title
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@ewels Does this generally look good? How do I trigger a rerun of the "nf-core branch protection" check? |
ewels
reviewed
May 27, 2023
| meta.single_end ? '' : (params.ignore_r2 > 0 ? "--ignore_r2 ${params.ignore_r2}" : ""), | ||
| meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_r2 ${params.ignore_3prime_r2}": "") | ||
| meta.single_end ? '' : (params.ignore_3prime_r2 > 0 ? "--ignore_3prime_r2 ${params.ignore_3prime_r2}": "") |
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i think #299 is linked to this
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@helenxl i believe its currently your github token permissions that are failing the tests but, I have a fix for this in #315 you can either update your github token permissions to write for pull_requests or I can roll these changes of yours into that maintenance PR if you like. let me know. looking forward to getting this merged |
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@sateeshperi Thanks! Your PR looks great. I will close this now. |
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--ignoreand--ignore_3prime) that were missing.--fastaflag is ignored when bismark aligner is used. This PR makes--fastaas a not required flag whenparams.aligneris bismark.PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).