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Add option to annotate vcf2cytosure file with different(customer) ids #521
Add option to annotate vcf2cytosure file with different(customer) ids #521
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Question about sample meta, otherwise it looks good.
ch_bam.combine(ch_vcf_tbi) | ||
.map { | ||
meta_sample, bam, meta_case, vcf, tbi -> | ||
new_meta = ['id':meta_sample.sample] |
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Won't this drop all the information that is in the bam meta aside from sample id? We need to preserve the sample meta as it contains information about the sample sex, which is used in the vcf2cytosure command, or att least transfer that key as well.
meta.sex.equals(1) ? '--sex male' : '--sex female', |
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Aah, good catch! Will fix it.
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👍
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).