nf-core/modules issues and pull requests

#3496 - Remove quay.io

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

#3495 - update gatk4/preprocessintervals

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

#3494 - Update sentieon modules

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

#3493 - Universc module update

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

#3492 - Upload on failure not naming artifact correctly

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

#3491 - CREATED histogram module

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

#3490 - new module: Metabuli

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

#3489 - fix: missing 'stub' option

Pull Request - State: closed - Opened by matq007 over 1 year ago

#3488 - Bcftools filter update

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

#3487 - Cutadapt missing stub

Pull Request - State: closed - Opened by matq007 over 1 year ago - 2 comments

#3486 - fix tests for kallistobustools, universc

Pull Request - State: closed - Opened by klkeys over 1 year ago
Labels: bug, tests

#3485 - Update UNIVERSC module

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

#3484 - add docker.io

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

#3483 - add docker.io

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

#3482 - New module: BACPHLIP

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

#3481 - Annotsv update

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

#3480 - FIX: remove mem assignement for SAMTOOLS_SORT

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

#3479 - FASTQ_ALIGN_BWAALN: Fixes bwa_aln subworkflow inconsistency with reads and the references they map against when multiple references supplied

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

#3478 - Scatterintervalsbyns

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

#3477 - Created fcs subworkflow

Pull Request - State: closed - Opened by scorreard over 1 year ago - 9 comments
Labels: Ready for Review, new subworkflow, subworkflows

#3476 - new module: HAPPY/REPPY

Issue - State: closed - Opened by LlaneroHiboreo over 1 year ago - 3 comments
Labels: new module

#3475 - new module: HAPPY/SOMPY

Issue - State: closed - Opened by LlaneroHiboreo over 1 year ago
Labels: help wanted, new module

#3474 - new module picard/scatterintervalsbyns

Pull Request - State: closed - Opened by nvnieuwk over 1 year ago - 4 comments
Labels: new module, Ready for Review

#3473 - FIX: Add error_retry label

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

#3472 - Add spaceranger

Pull Request - State: closed - Opened by grst over 1 year ago - 10 comments
Labels: Ready for Review

#3471 - Add default retry strategy to flaky bbsplit module

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

#3470 - bump fastp

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

#3469 - Fix bug in FASTQ_FASTQC_UMITOOLS_FASTP subworkflow

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

#3468 - Varlociraptor preprocess

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

#3467 - add varlociraptor estimate alignment properties

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

#3466 - Add kmcp profile

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

#3465 - Add purecn/normaldb test data to config and fix paths in tests

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

#3464 - suffix would be the extension of first file

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

#3463 - Controlfreec makegraph ploidy

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

#3462 - Fix pacbio modules

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

#3460 - Have Sentieon-modules support license in file

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

#3456 - SPADES changed flag for single-read in illumina reads

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

#3455 - [FEATURE] Disabling JVM Hotspot in modules for JAVA tools

Issue - State: open - Opened by lfearnley over 1 year ago - 5 comments

#3451 - Added genomad/download and genomad/endtoend modules

Pull Request - State: closed - Opened by CarsonJM over 1 year ago - 3 comments
Labels: new module, Ready for Review

#3443 - fix: correct alignment extension for bowtie2/align

Pull Request - State: closed - Opened by matq007 over 1 year ago - 10 comments

#3438 - salmon/quant update to handle multiple pairs of fastqs

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

#3436 - [FEATURE] accept multiple fastq pairs with salmon/quant

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

#3428 - add cramfilter module

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

#3424 - Updates for BGZIPTABIX

Pull Request - State: closed - Opened by DLBPointon over 1 year ago - 4 comments
Labels: enhancement

#3420 - new module: ncbi/datasetscli

Issue - State: open - Opened by charles-plessy over 1 year ago - 2 comments
Labels: new module

#3418 - new module: CLAME/binning

Issue - State: open - Opened by jeffe107 over 1 year ago
Labels: new module

#3409 - Update main.nf

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

#3406 - update expansionhunter docker

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

#3402 - add peka module

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

#3399 - new module: PEKA

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

#3394 - New module: samtools/cat

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

#3379 - add bed input to hsmetrics

Pull Request - State: closed - Opened by matthdsm over 1 year ago - 5 comments

#3362 - Newmoule nextdenovo

Pull Request - State: open - Opened by scorreard over 1 year ago - 7 comments
Labels: new module

#3350 - Output channel modification star

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

#3348 - Sentieon docker image

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

#3337 - fix corrected typo in output

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

#3334 - Make MAD plots optional in shinyngs

Pull Request - State: closed - Opened by pinin4fjords over 1 year ago - 3 comments

#3325 - feat added option of outputing wiggle and bedgraph

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

#3324 - Fix when not creating index with CRAM

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

#3303 - Update LAST modules to v1453

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

#3300 - Update bedtools map

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

#3297 - ADD MODULE: gnu/sort

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

#3295 - New Subworkflow: `fastq_ena_prep_adapterremoval_md5sum`

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

#3289 - BUSCO: additional outputs

Pull Request - State: closed - Opened by priyanka-surana over 1 year ago - 1 comment
Labels: update module

#3272 - New module: Mindagap/duplicatefinder

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

#3271 - new module: Mindagap/duplicatefinder

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

#3263 - gatk/markduplicatesspark: add bam index output

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

#3253 - new module: Picard positionbaseddownsamplesam

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

#3244 - Fixed the `amps` test

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

#3239 - New Module: Seqtk cutN

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

#3230 - bump snapaligner

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

#3228 - Migrate standalone tests to nf-test

Pull Request - State: closed - Opened by sateeshperi over 1 year ago
Labels: WIP

#3226 - Umitools extract subworkflow with splitting

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

#3224 - Sentieon dedup

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

#3222 - 3108 new module lofreq3

Pull Request - State: closed - Opened by VojislavLukic over 1 year ago - 4 comments
Labels: new module, hackathon2023

#3218 - New thermorawfileparser module

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

#3217 - [FEATURE] Update Pyrodigal module according to Prodigal

Issue - State: closed - Opened by jasmezz over 1 year ago
Labels: enhancement, hackathon2023

#3215 - update appropriate label for freyja boot

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

#3206 - sambamba sort module

Pull Request - State: open - Opened by BioInf2305 over 1 year ago

#3195 - Nv/2978 update index handling

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

#3190 - Add imaging test data in config

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

#3181 - New module: Hypo

Pull Request - State: closed - Opened by remiolsen over 1 year ago - 3 comments
Labels: new module, hackathon2023

#3177 - created epigen template

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

#3170 - Group all mus_musculus together

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

#3167 - new module: gridss/gridss_somatic_filter

Issue - State: open - Opened by kubranarci over 1 year ago
Labels: new module, hackathon2023

#3160 - 3084 new module svaba

Pull Request - State: closed - Opened by kubranarci over 1 year ago - 18 comments

#3157 - new module: FastQ-Screen

Issue - State: open - Opened by JPejovicApis over 1 year ago - 21 comments
Labels: hackathon2023

#3156 - new module: FastQ-Screen

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

#3154 - new module to convert mpileup to sync file

Issue - State: open - Opened by Ste40 over 1 year ago - 1 comment
Labels: new module, hackathon2023

#3140 - Purecn/run

Pull Request - State: closed - Opened by aldosr over 1 year ago - 5 comments
Labels: new module, hackathon2023

#3137 - Update params dependencies into value input channels #2982

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

#3133 - sambamba flagstat module

Pull Request - State: closed - Opened by kubranarci over 1 year ago - 1 comment
Labels: new module, hackathon2023

#3130 - New Subworkflow: Bam_trim_primers_ivar

Pull Request - State: open - Opened by Joon-Klaps over 1 year ago - 3 comments
Labels: new subworkflow, hackathon2023

#3129 - Purecn/normaldb

Pull Request - State: closed - Opened by aldosr over 1 year ago - 1 comment
Labels: new module, Ready for Review, hackathon2023

#3125 - Jpejovic update gatk tumor only subworkflow

Pull Request - State: open - Opened by JPejovicApis over 1 year ago - 1 comment
Labels: hackathon2023

#3121 - new module: KMCP/PROFILE

Issue - State: closed - Opened by jfy133 over 1 year ago
Labels: new module

#3106 - Cellranger arc module

Pull Request - State: closed - Opened by heylf over 1 year ago - 5 comments
Labels: new module, Do not merge yet, hackathon2023

#3105 - new module: thermorawfileparser

Issue - State: open - Opened by rolivella over 1 year ago - 2 comments
Labels: new module, hackathon2023

#3087 - new module: bioqc

Issue - State: open - Opened by pinin4fjords over 1 year ago - 1 comment
Labels: new module

#3081 - new module: HTSeq/count

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

GitHub / nf-core/modules issues and pull requests