Use bcftools/isec nf-core module for computing VCF intersection between multiple callers#47
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maxibor wants to merge 9 commits intonf-core:devfrom
Draft
Use bcftools/isec nf-core module for computing VCF intersection between multiple callers#47maxibor wants to merge 9 commits intonf-core:devfrom
maxibor wants to merge 9 commits intonf-core:devfrom
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added 6 commits
October 28, 2025 16:40
…8_bcftools_isec_nf_core
maxibor
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maxibor
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Please run |
famosab
reviewed
Oct 29, 2025
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@YussAb I already saw this with the template pr that the md5sums are not stable. I think we need to figure out why and if we can stabilize or assert differently. |
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famosab
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Feb 12, 2026
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I converted this to draft as we did some changes to the pipeline that we need to insert into this PR to make it work and we postpone this work for now :) |
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This PR replaces the python calling of bcftools isec in the
isec_vcfs.pyscript by the nf-core modules of bcftools isec.The main changes are:
This PR would close issue #28
This is work done at the Barcelona 2025 nf-core hackathon together with @eolaniru
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).CHANGELOG.mdis updated.