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

nf-core

*Pending review on nf-core/modules* - <https://github.com/organizations/nf-core/settings/reminders/65207|Manage reminder>  [#6659] <https://github.com/nf-core/modules/pull/6659|Script to fetch unique conda environments> (_ewels_)  _9 months stale · 2 years old ·_ Waiting on _infrastructure, ops_ [#8115] <https://github.com/nf-core/modules/pull/8115|ADDORREPLACEREADGROUPS and MERGEBAMALIGNMENT input/output file specificity fix.> (_johnoooh_)  _6 months stale · a year old ·_ Waiting on _<@UE6D8290F>, FriederikeHanssen_ [#8118] <https://github.com/nf-core/modules/pull/8118|MarkDuplicates Input specificity and input refactor. > (_johnoooh_)  _2 months stale · a year old ·_ Waiting on _<@UE6D8290F>_ [#8394] <https://github.com/nf-core/modules/pull/8394|Output interval_list file to channel for downstream processing> (_percyfal_)  _a year stale · a year old ·_ Waiting on _<@UE6D8290F>_ [#8433] <https://github.com/nf-core/modules/pull/8433|shellcheck: Run on .nf scripts> (_zeehio_)  _6 months stale · a year old ·_ Waiting on _ops_ [#8665] <https://github.com/nf-core/modules/pull/8665|Mixcr> (_derrik-gratz_)  _a month stale · a year old ·_ Waiting on _SPPearce_ [#9172] <https://github.com/nf-core/modules/pull/9172|adding homer merge peaks, and a peakcalling workflow> (_cmatKhan_)  _a year stale · a year old ·_ Waiting on _<@UV41DBFAT>_ [#9293] <https://github.com/nf-core/modules/pull/9293|Add nf-co2footprint plugin for emissions tracking> (_edmundmiller_)  _10 months stale · 10 months old ·_ Waiting on _infrastructure, ops_ [#9304] <https://github.com/nf-core/modules/pull/9304|fix: gprofiler2 output files missing gene names in intersection columns #497> (_mohe1linux_)  _5 months stale · 10 months old ·_ Waiting on _suzannejin, <@U02EXHZ4QRL>_ [#9338] <https://github.com/nf-core/modules/pull/9338|Use tar --no-same-owner option for untar module> (_nathanweeks_)  _2 months stale · 10 months old ·_ Waiting on _infrastructure, ops_ [#9360] <https://github.com/nf-core/modules/pull/9360|Add module: `TRIDENT_FETCH`> (_TCLamnidis_)  _a month stale · 10 months old ·_ Waiting on _itrujnara_ [#9504] <https://github.com/nf-core/modules/pull/9504|Get conda envs> (_mirpedrol_)  _9 months stale · 9 months old ·_ Waiting on _infrastructure, ops_ [#9967] <https://github.com/nf-core/modules/pull/9967|Module to build local snpEff database> (_pmoris_)  _2 months stale · 7 months old ·_ Waiting on _<@UE6D8290F>_ [#10305] <https://github.com/nf-core/modules/pull/10305|[GH-7778] Added matlock/bam2juicer> (_GallVp_)  _6 months stale · 6 months old ·_ Waiting on _atrigila_ [#10369] <https://github.com/nf-core/modules/pull/10369|feat(modules): add updhmm/vcfcheck> (_saraamenasantamaria_)  _11 days stale · 6 months old ·_ Waiting on _<@UE6D8290F>_ [#10379] <https://github.com/nf-core/modules/pull/10379|Add missing samplename from `generateReadgroupBCLCONVERT` metadata> (_tgelafr-pfzr_)  _6 months stale · 6 months old ·_ Waiting on _FloWuenne, matthdsm_ [#10403] <https://github.com/nf-core/modules/pull/10403|New Tool - pmlst> (_eit-maxlcummins_)  _5 months stale · 6 months old ·_ Waiting on _<@UQZG2UCF3>_ [#10587] <https://github.com/nf-core/modules/pull/10587|Remove SAMTOOLS_INDEX from BAM_SORT_STATS_SAMTOOLS workflow> (_yinshiyi_)  _6 months stale · 6 months old ·_ Waiting on _ljwharbers_ [#10656] <https://github.com/nf-core/modules/pull/10656|Add subtool cellranger aggregate> (_alenaboos_)  _4 months stale · 6 months old ·_ Waiting on _infrastructure, ops_ [#10788] <https://github.com/nf-core/modules/pull/10788|Update parabricks minimap2 for scnanoseq> (_gburnett-nvidia_)  _4 months stale · 6 months old ·_ Waiting on _atrull314, lianov_