Sawfish discover: allow genome.gclevels.mpack emission to be optional

[chaochaowong]

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[fellen31]

Is this for if you don't provide SNVs?

Looks ok, but seems like candidate.sv.bcf.csi is unstable in the snapshots. Could you change it to just check the name? Probably this wasn't caught before because the timestamp in the VCF header is a date.

[chaochaowong]

Is this for if you don't provide SNVs?

No. This change is for a test sample and config used in the pacvar pipeline (new release coming soon), where the sequencing coverage is low. If sawfish/discover runs with CNV enabled with low read coverage, it behaves similarly to hificnv and exits with status 65 due to insufficient coverage to determine CNV regions. Therefore, CNV must be disabled by setting ext.args = '--disable-cnv'.

When CNV is disabled, sawfish/discover does not produce several CNV-related outputs, including: copynum.bedgraph, copynum.mpack, sample.gcbias.mpack, and genome.gclevels.mpack. The emit option is already set to true for the first three files. I believe it is an oversight in the original module that genome.gclevels.mpack was not also marked as optional (emit: true), since it is likewise absent when CNV is disabled.

Looks ok, but seems like candidate.sv.bcf.csi is unstable in the snapshots. Could you change it to just check the name? Probably this wasn't caught before because the timestamp in the VCF header is a date.

Yes, I will edit main.nf.test so that it just check the name or file existance. [DONE]

Thank you so much for your feedback.