Add support for a regions bed to cuteSV: github.com/nf-core/modules/pull/13502

Li'l fix for matrix filtering in SummarizedExperiment: github.com/nf-core/modules/pull/13498

fix missing diagram in nextflow.config after template sync #C0493FQQZ3P github.com/nf-core/rnasplice/pull/349

Can someone please merge this tiny PR: https://github.com/nf-core/configs/pull/1153

Adding a different method for cnvkit in #C05GH685FKJ https://github.com/nf-core/createpanelrefs/pull/103/changes

Adding cnvkit targets for #C05GH685FKJ https://github.com/nf-core/createpanelrefs/pull/104/changes

Can I get a second review of my own template merge: https://github.com/nf-core/createtaxdb/pull/216 (@mashehu my Q is still outstanding for you on that one, about the nf-schema vrsion alignment)

little fix on #CE8SSJV3N to exclude samples that fail checks (mapping rate etc) from quantification and matrices: github.com/nf-core/rnaseq/pull/1984

... and another one to stop the rnaseq megatests failing with RSEM github.com/nf-core/rnaseq/pull/1959

Hi everyone! Time for a quick review here: github.com/nf-core/fastqrepair/pull/58 ?

Teensy-weensy documentation PR for #C062H82UCRG (3 lines): https://github.com/nf-core/createtaxdb/pull/222 if anyone feels bored on a sunday

Pending review on nf-core/modules · Manage reminder [#6659] Script to fetch unique conda environments (ewels) a year stale · 2 years old · Waiting on infrastructure, ops [#8115] ADDORREPLACEREADGROUPS and MERGEBAMALIGNMENT input/output file specificity fix. (johnoooh) 8 months stale · 2 years old · Waiting on @Maxime Garcia, FriederikeHanssen [#8284] Add eider modules (heuermh) 2 months stale · 2 years old · Waiting on @Edmund [#8394] Output interval_list file to channel for downstream processing (percyfal) a year stale · a year old · Waiting on @Maxime Garcia [#8433] shellcheck: Run on .nf scripts (zeehio) 8 months stale · a year old · Waiting on ops [#8500] Update RTN/TNI module (mribeirodantas) 2 months stale · a year old · Waiting on @Maxime Garcia [#8665] Mixcr (derrik-gratz) 4 months stale · a year old · Waiting on SPPearce [#9172] adding homer merge peaks, and a peakcalling workflow (cmatKhan) a year stale · a year old · Waiting on @Edmund [#9293] Add nf-co2footprint plugin for emissions tracking (edmundmiller) a year stale · a year old · Waiting on infrastructure, ops [#9304] fix: gprofiler2 output files missing gene names in intersection columns #497 (mohe1linux) 7 months stale · a year old · Waiting on suzannejin, @Susanne Jodoin [#9338] Use tar --no-same-owner option for untar module (nathanweeks) 4 months stale · a year old · Waiting on infrastructure, ops [#9504] Get conda envs (mirpedrol) a year stale · a year old · Waiting on infrastructure, ops [#9967] Module to build local snpEff database (pmoris) 4 months stale · 9 months old · Waiting on @Maxime Garcia [#10305] [GH-7778] Added matlock/bam2juicer (GallVp) 8 months stale · 8 months old · Waiting on atrigila [#10369] feat(modules): add updhmm/vcfcheck (saraamenasantamaria) 2 months stale · 8 months old · Waiting on @Maxime Garcia [#10379] Add missing samplename from `generateReadgroupBCLCONVERT` metadata (tgelafr-pfzr) 8 months stale · 8 months old · Waiting on FloWuenne, matthdsm [#10656] Add subtool cellranger aggregate (alenaboos) 7 months stale · 8 months old · Waiting on infrastructure, ops [#10788] Update parabricks minimap2 for scnanoseq (gburnett-nvidia) 6 months stale · 8 months old · Waiting on atrull314, lianov [#10988] Update atlas call (dangliu) 7 months stale · 7 months old · Waiting on SPPearce [#11014] UNZIP: modernize to latest nf-core conventions (maxcumminsandfred-lab) 7 months stale · 7 months old · Waiting on @Maxime Garcia

Hello, I have a couple of minor changes to push in #C06TRU74N4D

dev

branch before making a release PR for the 4.2.1 template update… github.com/nf-core/pairgenomealign/pull/169

Could I bump these two module PRs adding regions bed support to two structural variant callers: • Sniffles: github.com/nf-core/modules/pull/13501 • cuteSV: github.com/nf-core/modules/pull/13502

github.com/nf-core/test-datasets/pull/2358 Added bam files to test-dataset modules repo

new submodule for dartseq bullseeye part github.com/nf-core/modules/pull/13554

Hi!! Can I ask to merge github.com/nf-core/test-datasets/pull/1949 please 🙏? It's approved by piplus2 and all checks pass. Thank u 🙂

Hi everyone! Can I get a quick review here; github.com/nf-core/hic/pull/249

Adding missing citations nf-core/bacass 🙏: github.com/nf-core/bacass/pull/335

Addressing release review comments: https://github.com/nf-core/createpanelrefs/pull/109

back to dev PR: https://github.com/nf-core/createpanelrefs/pull/108

#C05GH685FKJ again, migrating to nf-schema 3.0.0: https://github.com/nf-core/createpanelrefs/pull/113

Hello, I made modules updates on #C02FC6VFQG1 before coming release of 2.1.0. Could anyone review it? I know it's a lot of files but it is "only" updated modules. github.com/nf-core/metatdenovo/pull/616 🙏

#C0493FQQZ3P can accept #C045UNCS5R9 samplesheet format github.com/nf-core/rnasplice/pull/350

Bump

cramino

version: github.com/nf-core/modules/pull/13559

Kindly request a review to allow alignment for methylation (conversion) data with bwa-mem3 github.com/nf-core/modules/pull/13560

New module hamronization/resfinder ready for review: nf-core/modules#13565 (test data in nf-core/test-datasets#2360)

I need help to get checkedfor a quick patch release github.com/nf-core/variantbenchmarking/pull/361

quick review for extending

nf-core modules bump-version

to also automatically bump it in the snapshot https://github.com/nf-core/tools/pull/4583

fix the labeler action in the modules repo to exclude conda-lock files from PR size calculations https://github.com/nf-core/modules/pull/13574