Add optional targets argument to CNVkit #13
Merged
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PR checklist
The current version of this tool defaults to the WGS method and has no option to pass the necessary target intervals for either hybrid method (which would be default of CNVkit) or amplicon method.
This PR simply adds a
cnvkit_targets
parameter, which can be used if the user wishes to default to the hybrid method. The channel defaults to the usual empty tuple, should the targets bed file not be provided, leaving the current execution as is.The modified pipeline has been successfully tested on real-life data, with either hybrid or current WGS method.
nf-core lint
): current version of dev - please note that some lint failures occur due to mismatch in templatenextflow run . -profile test,docker --outdir <OUTDIR>
).docs/usage.md
has been updated to explain the necessary modification of config file as well as the new optional parameter usage.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).