A community effort to collect a curated set of analysis pipelines built using Nextflow.

nf-core

MODULES BEING INCONSISTENT AS TO WHETHER THEY ARE TUMOUR THEN NORMAL OR NORMAL THEN TUMOUR FOR THEIR INPUT STRUCTURE

At least tumor/tumour doesn't impact the channel order

&gt; Normal then Tumour: 11 modules
&gt; • ascat
&gt; • biscuit/pileup
&gt; • controlfreec/freec
&gt; • deepsomatic
&gt; • manta/somatic
&gt; • msisensor/msi
&gt; • msisensorpro/msisomatic
&gt; • oncocnv
&gt; • sequenzautils/bam2seqz
&gt; • strelka/somatic
&gt; • varscan/somatic
&gt; Tumour then Normal: 9 modules
&gt; • cnvkit/batch
&gt; • lofreq/somatic
&gt; • muse/call
&gt; • parabricks/mutectcaller
&gt; • platypus (uses "control")
&gt; • savana/cna
&gt; • savana/run
&gt; • svaba
&gt; • telomerehunter (uses "control")
:neutral_face:

:shakefist: hackathon group to come up with yet another standard?

`val(meta), path(index_normal), path(input_tumour), path(input_normal), path(index_tumour)`

Screenshot 2026-08-27 at 18.02.52.png

claude just asking me the same thing :smile:

uhh, are you working on parabricks deepsomatic?

but I think tumour should come first :wink:

barely started (unless there is a PR somehwere already) , been doing a sweep on some of the parabricks stuff to clean up some of the implementation bits in sarek.

<https://github.com/nf-core/modules/pull/12797|github.com/nf-core/modules/pull/12797> I made a module :wink:

but couldn't convince the bot to make the snapshots

:woohoo: nice, should have made claude search PRs before thinking about input order