Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nf-core/modules issues and pull requests

#3926 - new module: cellranger/arc

Issue - State: closed - Opened by Joaodemeirelles about 1 year ago
Labels: new module

#3925 - Update seqkit modules to version 2.5.1

Pull Request - State: closed - Opened by heuermh about 1 year ago - 4 comments

#3924 - Update dsh-bio modules to version 2.3

Pull Request - State: closed - Opened by heuermh about 1 year ago - 1 comment

#3923 - bcftools/convert: add hap legend extension

Pull Request - State: closed - Opened by atrigila about 1 year ago
Labels: Ready for Review

#3922 - [FEATURE] bcftools/convert

Issue - State: closed - Opened by atrigila about 1 year ago
Labels: enhancement

#3921 - Update module propr/propd by adding updateF

Pull Request - State: closed - Opened by suzannejin about 1 year ago - 2 comments
Labels: ready to merge

#3919 - update taxpasta version

Pull Request - State: closed - Opened by LilyAnderssonLee about 1 year ago

#3918 - [FEATURE] subworkflows/multiple_impute_glimpse2

Issue - State: open - Opened by rflata about 1 year ago

#3917 - eggnogmapper module

Pull Request - State: open - Opened by vagkaratzas about 1 year ago

#3916 - Add purgedups histplot

Pull Request - State: closed - Opened by mahesh-panchal about 1 year ago
Labels: Ready for Review

#3915 - new module: PURGEDUPS/HISTPLOT

Issue - State: closed - Opened by mahesh-panchal about 1 year ago
Labels: new module

#3914 - Add tmp directory for temp output

Pull Request - State: open - Opened by weaglesBio about 1 year ago
Labels: update module, Ready for Review

#3912 - Fix CUSTOM/MATRIXFILTER

Pull Request - State: closed - Opened by WackerO about 1 year ago - 1 comment

#3911 - Different approach to handling sralite files when using prefetch.

Pull Request - State: closed - Opened by robsyme about 1 year ago - 1 comment

#3910 - new module: NeoLoopFinder

Issue - State: open - Opened by ninashenker about 1 year ago
Labels: new module

#3909 - Pairtools sort

Pull Request - State: closed - Opened by jianhong about 1 year ago - 4 comments

#3908 - Propr propd

Pull Request - State: closed - Opened by suzannejin about 1 year ago
Labels: new module

#3907 - Add spring/decompress module

Pull Request - State: closed - Opened by xec-cm about 1 year ago - 1 comment
Labels: Ready for Review, new subworkflow

#3906 - new subworkflow: spring/decompress

Issue - State: closed - Opened by xec-cm about 1 year ago
Labels: new subworkflow

#3905 - Update container build number

Pull Request - State: open - Opened by mahesh-panchal about 1 year ago - 6 comments

#3904 - Update FASTK_FASTK module to store and cleanup tmp files locally.

Issue - State: open - Opened by weaglesBio about 1 year ago
Labels: bug

#3903 - fastqc-nf-test : mv outputdir param to test file and add snapshot

Pull Request - State: closed - Opened by sateeshperi about 1 year ago - 2 comments

#3902 - gatk4/markduplicates: add stub

Issue - State: closed - Opened by rannick about 1 year ago

#3901 - fastqc/nf-test : params - add outputdir and add snapshot

Pull Request - State: closed - Opened by sateeshperi about 1 year ago

#3900 - add stub to gatk4 markduplicates

Pull Request - State: closed - Opened by rannick about 1 year ago
Labels: update module, Ready for Review

#3899 - Mmseqs/linclust

Pull Request - State: closed - Opened by vagkaratzas about 1 year ago

#3898 - Change proteus

Pull Request - State: closed - Opened by WackerO about 1 year ago - 3 comments

#3897 - Bug in stub section

Pull Request - State: closed - Opened by saulpierotti about 1 year ago
Labels: bug

#3895 - Update deprecated fastqc image

Pull Request - State: closed - Opened by gitanoqevaporelmundoentero about 1 year ago - 6 comments

#3894 - FGBIO: GroupByUMI module fix

Issue - State: open - Opened by FerriolCalvet about 1 year ago
Labels: update module

#3893 - Change fasta index channel

Pull Request - State: closed - Opened by LouisLeNezet about 1 year ago - 1 comment

#3892 - Fix variable typo in amrfinderplus/run

Pull Request - State: closed - Opened by jasmezz about 1 year ago - 1 comment

#3890 - Add config option to manta modules

Pull Request - State: closed - Opened by nvnieuwk about 1 year ago - 5 comments

#3889 - Blast

Pull Request - State: closed - Opened by vagkaratzas about 1 year ago

#3888 - Blastp

Pull Request - State: closed - Opened by vagkaratzas about 1 year ago

#3887 - Docker container megan `JavaFX detected no fonts` error

Issue - State: closed - Opened by MajoroMask about 1 year ago - 1 comment
Labels: bug

#3886 - update fcsadaptor

Pull Request - State: closed - Opened by yumisims about 1 year ago - 4 comments

#3885 - Add NONPAREIL

Pull Request - State: closed - Opened by jfy133 about 1 year ago

#3884 - Propr logratio

Pull Request - State: closed - Opened by suzannejin about 1 year ago
Labels: new module

#3883 - Modules stub

Pull Request - State: closed - Opened by LouisLeNezet about 1 year ago

#3882 - Fix linting ci

Pull Request - State: closed - Opened by mashehu about 1 year ago

#3881 - Picard/collectmultiplemetrics add optional to pdf output

Pull Request - State: closed - Opened by Joon-Klaps about 1 year ago - 2 comments

#3880 - Fix typo

Pull Request - State: closed - Opened by luisas about 1 year ago

#3879 - Picard collect multiplemetrics

Issue - State: closed - Opened by Joon-Klaps about 1 year ago
Labels: bug

#3878 - Add linting ci

Pull Request - State: closed - Opened by mashehu about 1 year ago

#3877 - Add missing output to linting CI

Pull Request - State: closed - Opened by mashehu about 1 year ago

#3876 - Update main.nf to include stub

Pull Request - State: closed - Opened by DLBPointon about 1 year ago - 1 comment
Labels: ready to merge

#3875 - Vcf impute glimpse multiple input bug correction

Pull Request - State: closed - Opened by LouisLeNezet about 1 year ago - 3 comments

#3874 - add UPP

Pull Request - State: open - Opened by lrauschning about 1 year ago - 1 comment

#3873 - update KrakenUniq version to the latest

Pull Request - State: closed - Opened by LilyAnderssonLee about 1 year ago

#3872 - new module: decoupleR

Issue - State: open - Opened by vicpaton about 1 year ago
Labels: new module

#3871 - Adding docker.io to container

Pull Request - State: closed - Opened by priyanka-surana about 1 year ago
Labels: WIP

#3870 - FIX: remove spaces in controlfreec modules

Pull Request - State: closed - Opened by maxulysse about 1 year ago

#3869 - Add samtools reheader

Pull Request - State: closed - Opened by LouisLeNezet about 1 year ago - 3 comments

#3868 - CUSTOM/MATRIXFILTER - NA handling

Pull Request - State: closed - Opened by WackerO about 1 year ago - 2 comments

#3867 - INITIALISE includes workflow logo

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 1 comment
Labels: ready to merge

#3866 - fix variable name

Pull Request - State: closed - Opened by mashehu about 1 year ago

#3865 - module for Sentieon tnhaplotyper2

Pull Request - State: closed - Opened by asp8200 about 1 year ago

#3864 - Add igenomes support in initialise

Issue - State: open - Opened by maxulysse about 1 year ago - 1 comment

#3863 - remove 'subworkflows/' prefix in linting command

Pull Request - State: closed - Opened by mashehu about 1 year ago

#3862 - Add license to cellranger count renaming script.

Pull Request - State: closed - Opened by grst about 1 year ago

#3861 - add linting for subworkflows to ci

Pull Request - State: closed - Opened by mashehu about 1 year ago

#3860 - Fix initialise linting

Pull Request - State: closed - Opened by mashehu about 1 year ago - 2 comments

#3859 - [FEATURE] output index files for GATK4_APPLYBQSR* modules

Issue - State: open - Opened by anoronh4 about 1 year ago

#3858 - Migrate chained modules tests to nf-test

Issue - State: open - Opened by Emiller88 about 1 year ago
Labels: tests

#3857 - Migrate subworkflow tests in nf-core/modules to nf-test

Issue - State: open - Opened by Emiller88 about 1 year ago
Labels: tests

#3856 - update umicollapse from process_medium to process_high

Pull Request - State: closed - Opened by CharlotteAnne about 1 year ago - 1 comment
Labels: ready to merge

#3855 - Tcoffee align

Pull Request - State: closed - Opened by luisas about 1 year ago

#3854 - new module: tcoffee/align

Issue - State: closed - Opened by luisas about 1 year ago
Labels: new module

#3853 - BRACKEN_BRACKEN: add extra missing output file

Pull Request - State: closed - Opened by jfy133 about 1 year ago

#3852 - INITIALISE uses take and emit

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 1 comment

#3851 - Sentieon tnhaplotyper2

Issue - State: open - Opened by asp8200 about 1 year ago

#3849 - Learnmsa align

Pull Request - State: closed - Opened by luisas about 1 year ago

#3848 - Add meta to bowtie build

Pull Request - State: open - Opened by SPPearce about 1 year ago

#3847 - Add INITIALISE subworkflow for starting nf-core pipelines

Pull Request - State: closed - Opened by adamrtalbot about 1 year ago - 6 comments

#3846 - Seqtk seq 1.4

Pull Request - State: closed - Opened by erikrikarddaniel about 1 year ago - 1 comment

#3845 - Expansionhunter 5.0.0

Pull Request - State: closed - Opened by nvnieuwk about 1 year ago - 1 comment

#3844 - FIX: Disable JVM hotspot in gatk4 modules

Pull Request - State: closed - Opened by maxulysse about 1 year ago - 3 comments

#3843 - add makegraph2

Pull Request - State: open - Opened by FriederikeHanssen about 1 year ago - 3 comments

#3842 - update version controlfreec

Pull Request - State: closed - Opened by FriederikeHanssen about 1 year ago

#3841 - Merge metas of guide tree and input fasta in famsa module (resubmitted)

Pull Request - State: closed - Opened by lrauschning about 1 year ago - 3 comments

#3840 - Integrate FASTA and guidetree meta in famsa module

Pull Request - State: closed - Opened by lrauschning about 1 year ago - 1 comment

#3839 - add MAGUS

Pull Request - State: open - Opened by lrauschning about 1 year ago - 8 comments

#3838 - Ngscheckmate fastq

Pull Request - State: closed - Opened by SPPearce about 1 year ago - 1 comment

#3837 - New module: GEM3

Pull Request - State: closed - Opened by miqalvarez about 1 year ago

#3836 - Update the biocontainer link

Pull Request - State: closed - Opened by LilyAnderssonLee about 1 year ago

#3835 - Add prefix to bwa/index

Pull Request - State: closed - Opened by nvnieuwk about 1 year ago - 3 comments

#3834 - bump shinyngs

Pull Request - State: closed - Opened by pinin4fjords about 1 year ago

#3833 - DRAFT: test of bcftools-sort

Pull Request - State: closed - Opened by asp8200 about 1 year ago

#3832 - Setting temp-dir for BCFTOOLS_SORT

Pull Request - State: closed - Opened by asp8200 about 1 year ago - 6 comments

#3831 - add module Retroseq Discover

Pull Request - State: open - Opened by peterpru about 1 year ago

#3830 - Update taxpasta version to 0.6.0

Pull Request - State: closed - Opened by LilyAnderssonLee about 1 year ago

#3828 - Pirate conda environment does not include the mcxdeblast binary

Issue - State: open - Opened by zachary-foster about 1 year ago - 1 comment
Labels: bug

#3827 - Update NGSCheckMate/ncm

Pull Request - State: closed - Opened by SPPearce about 1 year ago