nf-core/modules issues and pull requests

#3726 - Add sentieon dnamodelapply

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

#3725 - add module for abritamr_run

Pull Request - State: closed - Opened by rpetit3 over 1 year ago
Labels: ready to merge

#3724 - new module: abritamr/run

Issue - State: closed - Opened by rpetit3 over 1 year ago
Labels: new module

#3723 - Move conda-checks (seventh batch)

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

#3722 - Add sentieon dnascope

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

#3721 - Add sentieon readwriter

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

#3720 - Update Genrich module input tuple and argument

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

#3719 - Update other concoct containers

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

#3718 - Adding extra meta-fields for sentieon/dedup

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

#3717 - Adding extra meta-fields for sentieon/bwamem

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

#3716 - Adding extra meta-fields for sentieon/applyvarcal

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

#3715 - Add sentieon datametrics

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

#3714 - Add sentieon datametrics

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

#3713 - Move conda-checks (sixth batch)

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 2 comments

#3712 - Add seqkit/tab2fx module

Pull Request - State: closed - Opened by heuermh over 1 year ago - 1 comment
Labels: new module, Ready for Review

#3711 - Feature/extract align

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

#3710 - Extra parenthesis removed and added stub

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

#3709 - Add GATK's CreateReadCountPanelOfNormals and DenoiseReadCounts

Pull Request - State: closed - Opened by ramprasadn over 1 year ago - 4 comments

#3708 - Updating output-prefix for sentieon-bwaindex

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

#3707 - Update shinyngs, remove na.omit() from proteus

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

#3706 - Added new module csvtk/join

Pull Request - State: closed - Opened by anoronh4 over 1 year ago - 1 comment
Labels: new module, Ready for Review

#3705 - new module: csvtk/join

Issue - State: closed - Opened by anoronh4 over 1 year ago
Labels: new module

#3704 - Move conda-checks (fifth batch)

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

#3703 - Update bcftools stats

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

#3702 - add stub tests for two stubborn modules

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

#3701 - Updating multiqc to v1.15

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

#3700 - Added seqkit/fq2fa module

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

#3699 - Add module mmseqs easysearch

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

#3698 - new module: mmseqs/easysearch

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

#3697 - Add module famsa_align

Pull Request - State: closed - Opened by luisas over 1 year ago
Labels: new module, Ready for Review

#3696 - new module: famsa/align

Issue - State: closed - Opened by luisas over 1 year ago
Labels: new module, Ready for Review

#3695 - Missing input file channels in `bcftools/stats` module

Issue - State: closed - Opened by TCLamnidis over 1 year ago
Labels: bug

#3694 - Move conda-checks (fourth batch)

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

#3693 - Linting error related to GHCR container registry

Issue - State: closed - Opened by asp8200 over 1 year ago - 2 comments
Labels: bug

#3692 - Move conda-checks (third batch)

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

#3691 - ADD MODULE: Famsa guidetree

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

#3690 - Move conda-checks (second batch)

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

#3689 - Update MEGAHIT container URLs

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

#3688 - Picard MarkDuplicates fails when using conda profile because of wrong version installed

Issue - State: open - Opened by MRonzio over 1 year ago - 1 comment
Labels: bug

#3687 - new module: famsa/guidetree

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

#3686 - Move conda-checks (first batch)

Pull Request - State: closed - Opened by asp8200 over 1 year ago - 4 comments

#3685 - new module: seqtk/trim

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

#3684 - seqtk/trim

Issue - State: closed - Opened by Mahnaz-Shemirani over 1 year ago
Labels: new module

#3683 - Move conda-support in 44 modules

Issue - State: closed - Opened by asp8200 over 1 year ago - 1 comment
Labels: bug

#3682 - Add snakemake module

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

#3681 - Update kmcp profile

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

#3680 - Update kmcp modules

Pull Request - State: closed - Opened by sofstam over 1 year ago - 3 comments
Labels: update module

#3679 - Hierarchy of tests applied in order

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 8 comments

#3678 - Hierarchy of tests applied in order

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

#3677 - Github Actions uses fixed job names for branch protection rules

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

#3676 - changed to version 0.4.0

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

#3675 - Handle intervals + refactor

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

#3674 - Fix centrifuge: reduce number of input channels

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

#3673 - Fix invalid GATK container

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

#3672 - Modify subworkflows to pass new nf-core linting

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

#3671 - Update stubs for bwa mem

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

#3670 - Remove containers with cache with snpEff too

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

#3669 - Update CONCOCT_CONCOCT process label

Pull Request - State: open - Opened by prototaxites over 1 year ago - 2 comments
Labels: update module, Ready for Review

#3668 - Container image for deepvariant is not available

Issue - State: closed - Opened by fa2k over 1 year ago - 8 comments
Labels: bug

#3667 - Additional optional output to homer/annotatepeaks

Pull Request - State: closed - Opened by lnblum over 1 year ago - 1 comment
Labels: enhancement

#3666 - New module: galah

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

#3665 - Update stubs for samtools idxstats

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

#3664 - R differential modules control over output prefixes

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

#3663 - Update tiddit to v3.6.1

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

#3662 - TOPAS/GenConS

Pull Request - State: closed - Opened by aidaanva over 1 year ago - 7 comments

#3661 - update metaphlan module

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

#3660 - Update gatk3 modules

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

#3659 - gatk3 modules lack meta maps for additional files.

Issue - State: closed - Opened by TCLamnidis over 1 year ago
Labels: bug

#3658 - Bump ensembl-vep modules to 110.0

Pull Request - State: closed - Opened by maxulysse over 1 year ago - 1 comment
Labels: Do not merge yet

#3657 - Update stubs for samtools flagstat

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

#3656 - Hisat2 align splicesitesoptional

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

#3655 - Update: bamtools, gstama, ultra

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

#3654 - Multiple samtools modules use task.cpus-1 without checking for lower boundary

Issue - State: open - Opened by alexnater over 1 year ago
Labels: bug

#3653 - Hisat2 Align - optional inputs

Issue - State: closed - Opened by JackCurragh over 1 year ago
Labels: bug

#3652 - Update gecco/run

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

#3651 - CNVKit 0.9.10 update

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 7 comments

#3650 - Add seqkit/fx2tab module

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

#3649 - Hisat2-build: index construction w/ truly optional inputs

Pull Request - State: closed - Opened by JackCurragh over 1 year ago - 10 comments

#3648 - Hisat2 build optional inputs

Issue - State: closed - Opened by JackCurragh over 1 year ago
Labels: bug

#3647 - Prodigal - fails if input genome has same prefix

Issue - State: open - Opened by prototaxites over 1 year ago
Labels: bug

#3646 - Update bclconvert readme

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

#3645 - can not pull bclconvert image

Issue - State: closed - Opened by ludirm93 over 1 year ago - 3 comments
Labels: bug

#3644 - Bismark methylationextractor supplies unused "counts" argument

Issue - State: open - Opened by robsyme over 1 year ago - 1 comment

#3643 - Fix bug in pyrodigal module

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

#3642 - new module: samtools/import

Pull Request - State: closed - Opened by matthdsm over 1 year ago - 4 comments

#3641 - new module: TOPAS/GenConS

Issue - State: closed - Opened by aidaanva over 1 year ago
Labels: new module

#3640 - update icount mini version

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

#3639 - Bump taxpasta version (biocontainer not yet available)

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

#3638 - Fix/master commits

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

#3637 - Adding seqkit sliding command

Pull Request - State: closed - Opened by DLBPointon over 1 year ago - 1 comment
Labels: new module, Ready for Review

#3636 - update bcftools concat

Pull Request - State: open - Opened by nvnieuwk over 1 year ago - 2 comments

#3635 - Updated module: removed optional argument from mash/sketch

Pull Request - State: open - Opened by margotl9 over 1 year ago
Labels: update module

#3634 - Cooltools insulation

Pull Request - State: open - Opened by nservant over 1 year ago - 1 comment
Labels: new module

#3633 - Update vardictjava

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

#3632 - 3630 add unstitched reads as emitted output of ngmerge

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

#3631 - new module: Pairtools stats

Pull Request - State: closed - Opened by nservant over 1 year ago - 1 comment
Labels: new module, Ready for Review

#3630 - add unstitched reads as emitted output of ngmerge

Issue - State: closed - Opened by CharlotteAnne over 1 year ago

#3629 - new modules : Pairtools merge

Pull Request - State: closed - Opened by nservant over 1 year ago - 1 comment
Labels: new module, ready to merge

#3628 - new modules: Pairtools split

Pull Request - State: open - Opened by nservant over 1 year ago
Labels: new module, ready to merge

#3627 - [pairtools/sort] Update memory usage

Pull Request - State: closed - Opened by nservant over 1 year ago - 1 comment
Labels: update module, Ready for Review

GitHub / nf-core/modules issues and pull requests