fix Ascat R script execution

[ggabernet]

Fixes Ascat R script executions

PR checklist

• This comment contains a description of changes (with reason)
• If you've fixed a bug or added code that should be tested, add tests!
• If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repo
• Ensure the test suite passes (nextflow run . -profile test,docker).
• Make sure your code lints (nf-core lint .).
• Documentation in docs is updated
• CHANGELOG.md is updated
• README.md is updated

Learn more about contributing: CONTRIBUTING.md

[maxulysse]

Looks good, I'm just waiting if it works on our server as well, I'll likely merge it tomorrow

[maxulysse]

It would be good to finally manage to make files so that we could CI the ASCAT processes as well.

[maxulysse]

While we're at it, may I suggest we improve the ASCAT process with:

    purity_ploidy = (params.ascat_purity && params.ascat_ploidy) ? "--purity ${params.ascat_purity} --ploidy ${params.ascat_ploidy}" : ""
    """
    for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
    run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} ${purity_ploidy}
    """

to replace

sarek/main.nf

Lines 2598 to 2611 in d1a5691

	ascat_purity=params.ascat_purity
	ascat_ploidy=params.ascat_ploidy
	if (params.ascat_purity && params.ascat_ploidy)
	"""
	for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
	Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender} --purity ${ascat_purity} --ploidy ${ascat_ploidy}
	"""
	else
	"""
	for f in *BAF *LogR; do sed 's/chr//g' \$f > tmpFile; mv tmpFile \$f;done
	Rscript ${workflow.projectDir}/bin/run_ascat.r --tumorbaf ${bafTumor} --tumorlogr ${logrTumor} --normalbaf ${bafNormal} --normallogr ${logrNormal} --tumorname ${idSampleTumor} --basedir ${baseDir} --gcfile ${acLociGC} --gender ${gender}
	"""

[maxulysse]

But I could do that in a separate PR if you prefer

[ggabernet]

It's all good, however you like, let me just test first if the param name thing fixed the issue, then I can add it here

[ggabernet]

And I can also help with adding tests for ASCAT, if you like

[maxulysse]

And I can also help with adding tests for ASCAT, if you like

That would be amazing if we could do that

[maxulysse]

Worked on my side, with the _gc fix and the new purity_ploidy updated command.

[ggabernet]

ok just added your suggestion