Odgi stats consensus graphs #16
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I suspect https://github.com/nf-core/pangenome/pull/16/checks?check_run_id=1453281628 does not run through because of a too old Nextflow version? For me the following works: nextflow run main.nf --with-docker nfcore/pangenome:dev --input ../HLA-zoo/seqs/DRB1-3123.fa --do_stats |
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Maybe we need to bump the Nextflow version to a higher one, again? |
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Ok, now let me find the lowest Nextflow version number the tests run through. |
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I just figured that the next proper release after 20.07.1 is 20.10.0, so we have to stick with this one. |
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PR checklist
CHANGELOG.mdis updateddocsis updatedThis will take care of #10.
This PR only affects
main.nf.filewithpathto stick to the DSL2 standard as specified at https://www.nextflow.io/docs/latest/dsl2.html#dsl2-migration-notes.do_stats=false. If set to true,odgi statswill be executed for theseqwish, thesmoothxg, and theconsensusgraphs.consensus_jump_max. This specifies the maximum jump in nucleotides of a structural variant to include in the consensus graph. The argument is comma-separated. For each entry, a consensus graph will be generated and statistics will be produced, ifdo_stats=true.odgiStatsoutput is copied into the results folder underresults/odgiStats. Later in the development, the output of this channel will be forwarded toMultiQC.I was experimenting with
emitin order to bend Nextflow to my need. However, I am still lacking some experience working with Nextflow. So I suspect that my code does, what I intend it to do. But there might be a neater way in Nextflow to get there. Or I don't stick to some formatting standards. Happy to learn!