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

#3626 - Newmodule ngmerge

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

#3625 - new module: NGMERGE

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

#3624 - NEW MODULE: PURECLIP

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

#3623 - New module: instrain/compare

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

#3620 - fix integer overflow

Pull Request - State: closed - Opened by sstrong99 over 1 year ago

#3619 - Adding modules from #scrnaseq for simpleaf

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

#3618 - Barrnap

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

#3617 - new module: barrnap

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

#3616 - nf-core plasflow module

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

#3615 - Update manta modules

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

#3614 - Transfer mutect2 SBWFs from sarek

Pull Request - State: open - Opened by maxulysse over 1 year ago - 3 comments

#3613 - Arcashla genotype

Pull Request - State: open - Opened by mapo9 over 1 year ago - 1 comment

#3612 - add new module iCount-mini/metagene

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

#3611 - new module: ICOUNTMINI/METAGENE

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

#3610 - Update md5sum module to be able to take multiple files

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

#3609 - Add mapAD/map

Pull Request - State: closed - Opened by jch-13 over 1 year ago

#3608 - new module: PLOTHEATMAP

Issue - State: open - Opened by bozmik over 1 year ago - 4 comments
Labels: new module

#3607 - new module: PURECLIP

Issue - State: closed - Opened by CharlotteAnne over 1 year ago
Labels: new module, WIP

#3606 - bam_markduplicates_samtools

Pull Request - State: closed - Opened by priyanka-surana over 1 year ago - 2 comments
Labels: new subworkflow

#3605 - Update bcftools query

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

#3604 - Metaphlan4 update: add --index

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

#3603 - New module: mmseqs/createtsv

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

#3602 - Charliecloud can't pull biocontainers images

Issue - State: open - Opened by Mia0509 over 1 year ago - 2 comments
Labels: bug

#3601 - new module: mmseqs2/createdb

Pull Request - State: closed - Opened by Joon-Klaps over 1 year ago
Labels: new module

#3600 - New module: mmseqs/cluster

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

#3599 - new module: MMSEQS/CREATEDB

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

#3598 - update eklipse

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

#3597 - new module: MMSEQS/CLUSTER

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

#3596 - update postprocessgermlinecnvcalls

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

#3595 - New module: mmseqs/search

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

#3594 - License on sentieon script

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

#3593 - Use `gzip -cd` because `gunzip` preserves the group ownership

Pull Request - State: closed - Opened by muffato over 1 year ago - 6 comments
Labels: Ready for Review

#3592 - add module for pneumocat

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

#3591 - new module: PneumoCAT

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

#3590 - sub-tool names must be one word - msisensorpro/msisomatic

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

#3588 - Ucsc update

Pull Request - State: closed - Opened by DLBPointon over 1 year ago - 2 comments
Labels: enhancement, Ready for Review

#3587 - Windowmasker update

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

#3586 - Bump taxpasta version

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

#3585 - Add geoquery/getgeo

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

#3584 - Update germlinecnvcaller

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

#3583 - New module: emboss/cons

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

#3582 - new module: EMBOSS/cons

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

#3581 - Gcnvcaller modules

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

#3580 - change authorship

Pull Request - State: closed - Opened by mapo9 over 1 year ago - 2 comments

#3579 - Update genmap modules

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

#3578 - Add proteus module

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

#3577 - Freyja doc meta fix

Pull Request - State: open - Opened by Joon-Klaps over 1 year ago - 1 comment
Labels: documentation

#3576 - New Cellrangerarc modules

Pull Request - State: open - Opened by heylf over 1 year ago - 2 comments
Labels: Do not merge yet

#3575 - New Cellranger-atac modules

Pull Request - State: open - Opened by heylf over 1 year ago - 4 comments
Labels: Do not merge yet

#3574 - Fastq screen

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

#3573 - Add mitohifi/mitohifi module

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

#3566 - new module: gem2/gem_2_bed_mappability

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

#3563 - Add link to README

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

#3561 - update modules in GATK's gcnvcaller pipeline

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

#3560 - Update rgi/main

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

#3558 - Bump b2fq

Pull Request - State: open - Opened by Emiller88 over 1 year ago - 8 comments

#3555 - Adding module for cram-size command of samtools

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

#3551 - Ashlar

Pull Request - State: closed - Opened by RobJY over 1 year ago - 26 comments
Labels: Ready for Review, imaging

#3550 - new module: ASHLAR

Issue - State: closed - Opened by RobJY over 1 year ago - 2 comments
Labels: new module

#3545 - upgrade CNVkit to 0.9.10

Pull Request - State: closed - Opened by priesgo over 1 year ago - 2 comments
Labels: bug, help wanted, update module

#3544 - CNVkit batch module went through an uncontrolled pandas upgrade which makes it crash

Issue - State: closed - Opened by priesgo over 1 year ago
Labels: bug, update module

#3538 - new subworkflow bam_cnv_wisecondorx

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

#3537 - Automatically rename input files in cellranger module

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

#3533 - new subworkflow: bam_cnv_wisecondorx

Issue - State: closed - Opened by nvnieuwk over 1 year ago
Labels: new subworkflow

#3530 - add varlociraptor tmb sceleton, need testing file

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

#3529 - add varlociraptor call subcommand

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

#3527 - fix errors according to schema

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

#3526 - Umitools/dedup adding log and bug workaround

Pull Request - State: open - Opened by anoronh4 over 1 year ago - 1 comment
Labels: Ready for Review

#3525 - Fix metaeuk_easypredict when using mmseqs database

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

#3524 - new module: ctat

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

#3523 - Minor fixes.

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

#3522 - Adding upd

Pull Request - State: closed - Opened by hrydbeck over 1 year ago
Labels: draft

#3521 - Speed up GATK4 MD with CRAM & fix MDSpark version

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

#3520 - Fix tag quotes in mmseqs_databases

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

#3519 - Trying the latest bioconda recipe for Sentieon

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

#3518 - Update ganon/classify to include a log file

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

#3517 - update sentieon/modules to use quay.io

Pull Request - State: closed - Opened by maxulysse over 1 year ago - 6 comments

#3516 - Update ataqv modules version

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

#3515 - Add a test for CRAM files for NGSCheckMate

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

#3514 - Add stub for kmcp profile

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

#3513 - Add stub for kmcp search module

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

#3512 - Add test for stub for kmcp index module

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

#3511 - New module: MetaEuk easypredict

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

#3510 - Add stub to kmcp compute module

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

#3509 - add args and memory for cdhit

Pull Request - State: closed - Opened by Joon-Klaps over 1 year ago - 1 comment
Labels: bug, enhancement

#3508 - correctly set memory in gatk4/createsequencedictionary

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

#3507 - Fix inclusion of input bams in work directory

Pull Request - State: closed - Opened by anoronh4 over 1 year ago - 3 comments
Labels: Ready for Review

#3506 - Add log file in output channels of umitools/dedup

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

#3504 - umitools/dedup converts input bam from symlink to hard link

Issue - State: open - Opened by anoronh4 over 1 year ago - 1 comment
Labels: bug

#3503 - NEW module for predicting bacterial host of phages: iPHoP

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

#3502 - FIX: Fix memory issue with some gatk4 modules

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

#3501 - New module: mmseqs_databases

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

#3500 - adding seqkit grep

Pull Request - State: closed - Opened by Joon-Klaps over 1 year ago
Labels: new module

#3499 - Add singularity.registry = 'quay.io' for tests

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

#3498 - new module: ALLCatchR

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

#3497 - Move containers for sarek, demultiplex and scrnaseq to quay.io

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