Re: Netflow with nf-core as possible workflow targets

[Steffen Möller <steffen_moeller@gmx.de>]

Hello again,

On 02.05.19 16:55, Steffen Möller wrote:
> 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.

Alex of the nf-core folks had kindly pointed me to
https://github.com/nf-core/test-datasets . Every workflow of theirs uses
a branch of that repository for their CI testing. This is rather neat.

Best,

Steffen