nf-core/modules issues and pull requests

#3078 - new module: sigprofilerextractor

Issue - State: open - Opened by FerriolCalvet over 1 year ago
Labels: new module

#3063 - New fastq_fastqc_umitools_fastp subworkflow

Pull Request - State: closed - Opened by robsyme over 1 year ago - 2 comments
Labels: Ready for Review, new subworkflow

#3062 - Add logic to filter reads based on read count after trimming to fastq_fastqc_umitools_trimgalore subworkflow

Pull Request - State: closed - Opened by robsyme over 1 year ago
Labels: Ready for Review, update subworkflow

#3061 - Sniffles

Pull Request - State: closed - Opened by yuukiiwa over 1 year ago

#3060 - add pepper_margin_deepvariant

Pull Request - State: open - Opened by yuukiiwa over 1 year ago

#3059 - Cutesv

Pull Request - State: closed - Opened by yuukiiwa over 1 year ago - 2 comments

#3058 - Clair3

Pull Request - State: open - Opened by yuukiiwa over 1 year ago

#3054 - Fix seg-faults introduced in STAR 2.7.10a

Pull Request - State: open - Opened by jma1991 over 1 year ago - 1 comment

#3034 - Drop

Pull Request - State: open - Opened by TheMarshalMole over 1 year ago - 1 comment

#3020 - new module: Emu

Issue - State: open - Opened by fwa93 over 1 year ago
Labels: new module

#3019 - update vcf_gather_bcftools subworkflow acc. to nf-core guidelines

Pull Request - State: open - Opened by ramprasadn over 1 year ago - 1 comment

#3018 - update fastq_download_prefetch_fasterqdump_sratools subworkflow acc. to guidelines

Pull Request - State: open - Opened by ramprasadn over 1 year ago
Labels: Ready for Review, update subworkflow

#3017 - update fastq_align_chromap subworkflow acc. to nf-core guidelines

Pull Request - State: open - Opened by ramprasadn over 1 year ago
Labels: Ready for Review, update subworkflow

#3014 - Update bam_qc_picard subworkflow acc. to nf-core guidelines

Pull Request - State: open - Opened by ramprasadn over 1 year ago
Labels: Ready for Review, update subworkflow

#3010 - Pairtools stats

Pull Request - State: closed - Opened by jianhong over 1 year ago - 1 comment

#3008 - Centrifuge db build

Pull Request - State: open - Opened by sarah-buddle over 1 year ago

#2991 - update fastq_contam_seqtk_kraken to guidelines

Pull Request - State: open - Opened by nvnieuwk over 1 year ago
Labels: subworkflows, ready to merge

#2988 - update fasta binning concoct to guidelines

Pull Request - State: open - Opened by nvnieuwk over 1 year ago
Labels: Ready for Review, subworkflows

#2968 - feat: add parabricks/haplotypecaller

Pull Request - State: open - Opened by bsiranosian over 1 year ago - 7 comments

#2967 - feat: add parabricks/deepvariant

Pull Request - State: open - Opened by bsiranosian over 1 year ago

#2966 - feat: add parabricks/mutectcaller

Pull Request - State: open - Opened by bsiranosian over 1 year ago - 1 comment

#2965 - Update fastqc version

Pull Request - State: open - Opened by ekushele over 1 year ago - 6 comments

#2955 - New module: kaiju/mkbwt and kaiju/mkfmi

Issue - State: closed - Opened by sarah-buddle over 1 year ago - 1 comment
Labels: new module, hackathon2023

#2950 - Pairtools sample

Pull Request - State: open - Opened by jianhong over 1 year ago - 1 comment

#2949 - add module hicexplorer/hicplotmatrix

Pull Request - State: open - Opened by jianhong over 1 year ago

#2947 - Hicexplorer hiccorrectmatrix

Pull Request - State: open - Opened by jianhong over 1 year ago

#2944 - add module hicexplorer/hicfindtads

Pull Request - State: open - Opened by jianhong over 1 year ago - 1 comment
Labels: Ready for Review

#2940 - new module: purecn/run

Issue - State: closed - Opened by lbeltrame over 1 year ago
Labels: new module, hackathon2023

#2939 - new module: purecn/normaldb

Issue - State: closed - Opened by lbeltrame over 1 year ago
Labels: new module, hackathon2023

#2933 - Hicexplorer hicpca

Pull Request - State: closed - Opened by jianhong over 1 year ago - 1 comment
Labels: Ready for Review

#2902 - feat: add stats parameter support to FilterMutectCalls

Pull Request - State: open - Opened by lmtani almost 2 years ago - 8 comments

#2880 - add stale GHA

Pull Request - State: open - Opened by mirpedrol almost 2 years ago

#2878 - new subworkflow vcf_merge_jasmine

Pull Request - State: open - Opened by nvnieuwk almost 2 years ago
Labels: WIP, new subworkflow

#2859 - Cooltools eigscis

Pull Request - State: open - Opened by jianhong almost 2 years ago

#2849 - Nanomonsv get

Pull Request - State: open - Opened by awgymer almost 2 years ago

#2843 - make fasta optional; remove fai

Pull Request - State: open - Opened by wikiselev almost 2 years ago - 1 comment

#2842 - add --target-file argument

Pull Request - State: open - Opened by wikiselev almost 2 years ago - 1 comment

#2837 - New module: custom/splitfastqbylane

Pull Request - State: open - Opened by anoronh4 almost 2 years ago

#2835 - New module: tiledbvcf

Pull Request - State: open - Opened by atrigila almost 2 years ago - 2 comments
Labels: WIP

#2830 - Cooltools pileup

Pull Request - State: open - Opened by jianhong almost 2 years ago

#2828 - Ciriquant

Pull Request - State: open - Opened by BarryDigby almost 2 years ago
Labels: WIP

#2806 - new module: bayestyper/genotype

Issue - State: open - Opened by nvnieuwk almost 2 years ago
Labels: new module

#2804 - new module: kmc

Issue - State: open - Opened by nvnieuwk almost 2 years ago
Labels: new module

#2783 - Add spring/compress module

Pull Request - State: closed - Opened by xec-cm almost 2 years ago - 6 comments
Labels: ready to merge

#2782 - Add new module vgan/haplocart

Pull Request - State: open - Opened by JoshuaDanielRubin almost 2 years ago - 14 comments

#2770 - new module: spring

Issue - State: closed - Opened by xec-cm almost 2 years ago
Labels: new module

#2768 - new subworkflow: vcf_validate_small_variants

Pull Request - State: open - Opened by nvnieuwk almost 2 years ago - 2 comments
Labels: WIP, new subworkflow

#2767 - Module: ichorcna/run updated to v0.5.0

Pull Request - State: open - Opened by adamrtalbot almost 2 years ago - 7 comments

#2762 - Failed to create MultiQC 1.14 conda environment

Issue - State: open - Opened by ekushele almost 2 years ago - 1 comment
Labels: bug

#2741 - Fix #2154

Pull Request - State: closed - Opened by muffato almost 2 years ago

#2738 - Greater than 256

Pull Request - State: open - Opened by Emiller88 almost 2 years ago

#2720 - Allow version stripping from features for GSEA

Pull Request - State: open - Opened by pinin4fjords almost 2 years ago

#2703 - enhancement: add parameter for fastp to make writing of trimmed fastqs optional

Pull Request - State: open - Opened by anoronh4 almost 2 years ago - 4 comments
Labels: enhancement, Ready for Review

#2702 - add module for stecfinder

Pull Request - State: closed - Opened by rpetit3 almost 2 years ago
Labels: new module, ready to merge

#2701 - new module: stecfinder

Issue - State: closed - Opened by rpetit3 almost 2 years ago
Labels: new module

#2694 - add modules for sra-human-scrubber

Pull Request - State: open - Opened by rpetit3 almost 2 years ago

#2675 - Configure testing with Podman and Mamba

Pull Request - State: open - Opened by TomKellyGenetics almost 2 years ago - 4 comments
Labels: tests, WIP, draft

#2674 - Update samtools_view

Pull Request - State: open - Opened by priyanka-surana almost 2 years ago - 2 comments
Labels: help wanted, update module

#2664 - Add module Emboss/getorf

Pull Request - State: open - Opened by timslittle almost 2 years ago

#2590 - new module: Tiara

Issue - State: open - Opened by eeaunin almost 2 years ago - 1 comment
Labels: new module

#2572 - new module: HyPo

Issue - State: closed - Opened by diegomics almost 2 years ago
Labels: new module

#2571 - new module: MitoHiFi

Issue - State: closed - Opened by mahesh-panchal almost 2 years ago - 4 comments
Labels: new module

#2495 - bump svdb version

Pull Request - State: open - Opened by FriederikeHanssen about 2 years ago - 3 comments

#2450 - Cellranger-atac module

Pull Request - State: closed - Opened by heylf about 2 years ago - 7 comments
Labels: new module, Ready for Review, Do not merge yet

#2341 - Migrate to nf-test meta Issue

Issue - State: open - Opened by Emiller88 about 2 years ago - 15 comments
Labels: tests, hackathon2023

#2332 - new module: MMSEQS/SEARCH

Issue - State: closed - Opened by JoseEspinosa about 2 years ago - 1 comment
Labels: new module

#2318 - Dedup subworkflow name

Pull Request - State: open - Opened by SPPearce about 2 years ago - 16 comments

#2291 - refactor: Support container_registry in modules

Pull Request - State: closed - Opened by Emiller88 about 2 years ago - 43 comments
Labels: WIP, update module

#2231 - New module: presto/filterseq

Pull Request - State: open - Opened by snafees about 2 years ago - 2 comments

#2206 - Bbmap filterbyname

Pull Request - State: open - Opened by tokarevvasily about 2 years ago - 9 comments

#2196 - new module: orthofinder/orthofinder

Issue - State: open - Opened by baptisteImbert about 2 years ago
Labels: new module

#2154 - Fix tests after modules repository restructuring

Issue - State: open - Opened by JoseEspinosa about 2 years ago - 6 comments
Labels: bug, tests

#1990 - new module: sentieon/GVCFtyper

Issue - State: closed - Opened by ashotmarg about 2 years ago - 2 comments
Labels: new module

#1964 - Add in path to all files in index directory to copy on Azure correctly.

Pull Request - State: open - Opened by vsmalladi over 2 years ago - 7 comments
Labels: update module, Do not merge yet

#1942 - Add splice junctions input to STAR align

Pull Request - State: open - Opened by cguyomar over 2 years ago
Labels: update module

#1940 - New Module: YAHA

Pull Request - State: open - Opened by cmatKhan over 2 years ago - 1 comment
Labels: new module, WIP

#1937 - [COOLER] new functions - balance / makebins

Pull Request - State: closed - Opened by nservant over 2 years ago - 9 comments
Labels: new module, WIP

#1785 - Goalign cleanseqs

Pull Request - State: open - Opened by andersgs over 2 years ago - 4 comments
Labels: new module

#1679 - humann3

Pull Request - State: closed - Opened by kohjy-ag over 2 years ago - 3 comments
Labels: new module, WIP, stale

#1593 - new module: nonpareil

Issue - State: closed - Opened by jfy133 over 2 years ago - 2 comments
Labels: new module

#1403 - new module: MetaMaps

Issue - State: closed - Opened by henningonsbring over 2 years ago
Labels: new module

#1160 - new module: staramr

Issue - State: closed - Opened by rpetit3 almost 3 years ago - 4 comments
Labels: new module, stale

#977 - Add new module: Bustools sort

Pull Request - State: closed - Opened by tkhalilullah about 3 years ago - 5 comments
Labels: new module, WIP, RIP, stale

#917 - Nanopolish by the encore

Pull Request - State: open - Opened by projectoriented about 3 years ago - 2 comments
Labels: new module, WIP

#734 - new module: sentieon/dedup

Issue - State: closed - Opened by Gwennid about 3 years ago - 3 comments
Labels: new module, hackathon2023

#733 - new module: sentieon/locuscollector

Issue - State: closed - Opened by Gwennid about 3 years ago - 5 comments
Labels: new module, hackathon2023

#732 - new module: sentieon/bwamem

Issue - State: closed - Opened by Gwennid about 3 years ago - 5 comments
Labels: new module, hackathon2023

#258 - [FEATURE]: Ask for slightly less memory for tools with explicit task.memory definitions

Issue - State: open - Opened by drpatelh over 3 years ago - 11 comments
Labels: hackathon2023

#91 - Add CODEOWNERS

Pull Request - State: closed - Opened by Emiller88 almost 4 years ago - 14 comments
Labels: enhancement, help wanted, stale

GitHub / nf-core/modules issues and pull requests