Netflow with nf-core as possible workflow targets
Hello,
The nextflow folks have recently published a preprint on their nf-core
(https://nf-co.re/) effort to host routine workflows in bioinformatics.
Reserachgate kindly pointed me to it:
https://github.com/nf-core/rnaseq/blob/master/environment.yml
I had a random pick on
https://github.com/nf-core/rnaseq/blob/master/environment.yml to learn
about requirements of their rnaseq workflow. Very close we are -the
effort we keep investing into getting bcbio completely functional helped
here. But a few are still missing:
bioconductor-dupradar
https://bioconductor.org/packages/release/bioc/html/dupRadar.html
csvtk https://github.com/shenwei356/csvtk
preseq http://smithlabresearch.org/software/preseq/
rseqc http://rseqc.sourceforge.net/
deeptools https://github.com/deeptools/deepTools
and others like
multiqc
gffread
are already in the making.
I admit not to know about how to best invest our resources here. But if
there are readers of this list who use nextflow already - please speak
and sync up - with us and them.
Best,
Steffen
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