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Add fastq seqkit sana pair #9185
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Looking really good @vagkaratzas! A few minor comments/questions
Co-authored-by: James A. Fellows Yates <[email protected]>
…ing strandness on the meta
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LGTM!
Two minor comments - I don't think they're blocking, but definitely the config file one would IMO be nice-to-have.
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Same as Jim, no major blockers now
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Thank you both! |
* FASTQ_SEQKIT_SANA_PAIR subworkflow init * more tests and meta added * unnecessary operations removed * in one line * Update subworkflows/nf-core/fastq_seqkit_sana_pair/main.nf Co-authored-by: James A. Fellows Yates <[email protected]> * meta descr and keywords updated * descr updated * renamed and removed the copying mechanism, replaced with adding/removing strandness on the meta * mandatory config * meta single_end checks --------- Co-authored-by: James A. Fellows Yates <[email protected]>
New
fastqfile sanitization/pre-processing subworkflow, to be used instead of justseqkit/sana, that automatically breaks paired-end reads (seqkit/sanacan only process one file at a time), mixes with single-end reads in one channel, runsseqkit/sanaand finally merges back original pairs withseqkit/pair.PR checklist
versions.ymlfile.labelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile condanf-core subworkflows test <SUBWORKFLOW> --profile dockernf-core subworkflows test <SUBWORKFLOW> --profile singularitynf-core subworkflows test <SUBWORKFLOW> --profile conda