Generate Genomeqc samplesheet - #215
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erikrikarddaniel
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Tiny suggestion, otherwise great.
Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
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Given the recent release of nf-core/genomeqc, preparation of a samplesheet for downstream genomeqc was proposed (#214).
This PR adds an extra output, compatible with the (updated) downstream samplesheet in the form of
assembly,fasta.Trying to implement this has uncovered a bunch of inconsistencies, which are fixed here:
The placeholder channel that contains all final scaffolds (there is nothing downstream currently), was misformatted and contained a nested map. This has been fixed in
subworkflows/scaffold/main.nf. There was also a problem in one of the nested scaffolding workflows (ragtag) which did not emit the correct elementThe local
BGZIPprocess, which ensures that all assemblies are bgzipped for samtools compatibility emits a folder (out/file.gz), I had not realized that this will publish the same folder structure, and not simply the file. Fixed via fixes toconfig/filespublishDirdirectivesusage.mdwas updatedCHANGELOG.mdwas updatedTest snapshots were updated.