fixing prefixing issue #21
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@fellen31 my solution should preserve the same order as join joins on meta. @maxulysse I will add the add to the change log! |
Yes, but after the join, what keeps |
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Okay - I switched to using multiMap and updated the CHANGELOG (including changes from a previous PR where I did not update the changelog - #19 . Thanks!! |
| //join the bam and bai and vcf based off the meta id (ensure correct order) | ||
| bam_bai_vcf_ch = bam_bai_ch.join(BAM_SV_VARIANT_CALLING.out.vcf_ch) | ||
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| bam_bai_vcf_ch | ||
| .multiMap { meta, bam, bai, vcf, tbi -> | ||
| bam_bai: [meta, bam, bai] | ||
| vcf_tbi: [meta, vcf, tbi] | ||
| } | ||
| .set { orderd_bam_bai_vcf_tbi } | ||
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I would be a bit careful naming the channels containing SNPs and SVs the same.
Perhaps you could for example have bam_bai_vcf_snp_ch and bam_bai_vcf_sv_ch etc. so that someone not as familiar with the code can more easily distinguish them?
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Have modified according to your suggestion!
Co-authored-by: Felix Lenner <[email protected]>
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,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).This PR should just ensure that for Hiphase, the VCF and BAM and BAI channels are correctly ordered such that the orders correspond to the same file prefix