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

#4301 - Apptainer error

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

#4300 - chore(deps): update dependency bioconda/samtools to v1.18

Pull Request - State: open - Opened by renovate[bot] about 1 year ago

#4299 - Fix conda and renovate

Pull Request - State: closed - Opened by Emiller88 about 1 year ago

#4298 - build: Add renovate comments to conda packages

Pull Request - State: closed - Opened by Emiller88 about 1 year ago

#4297 - Add renovate config check

Pull Request - State: closed - Opened by Emiller88 about 1 year ago - 5 comments

#4296 - Update missed renovate environments

Pull Request - State: closed - Opened by Emiller88 about 1 year ago

#4295 - update multiqc to 1.17 in custom/dumpsoftwareversions

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

#4294 - Add gprofiler2 module

Pull Request - State: open - Opened by WackerO about 1 year ago - 1 comment
Labels: question, Ready for Review

#4293 - Update samtools in svdb

Issue - State: closed - Opened by FriederikeHanssen about 1 year ago - 1 comment

#4292 - Update samtools in samblaster

Issue - State: closed - Opened by FriederikeHanssen about 1 year ago - 1 comment

#4291 - add variants_command for optionnal germline ressource reference

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

#4290 - update multiqc to 1.17 in custom/dumpsoftwareversions

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

#4289 - Update mosdepth to 3.5

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

#4288 - Update samtools to 1.17 in dragmap/align

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

#4287 - Update samtools to 1.17 in bwamem2/mem

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

#4286 - Update samtools to 1.17 in bwa/mem

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

#4285 - Added a meta map for the reference genome of minimap2

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

#4284 - ci: One changes job to rule them all

Pull Request - State: open - Opened by Emiller88 about 1 year ago

#4283 - new module: vcf2cytosure

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

#4282 - FIX: More coherence in all gatk4spark modules

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

#4281 - chore(deps): update biocontainers/kmcp docker tag to v0.9.4

Pull Request - State: open - Opened by renovate[bot] about 1 year ago

#4280 - add arriba download

Pull Request - State: open - Opened by peterpru about 1 year ago - 1 comment
Labels: new module

#4279 - chore(deps): Bump checkm-genome conda env

Pull Request - State: closed - Opened by Emiller88 about 1 year ago

#4278 - Can we have sorted channels with linting?

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

#4277 - Update samtools to 1.17 in svdb/merge

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

#4276 - Update samtools to 1.17 in samblaster

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

#4274 - update gatk4/applybqsrspark to 4.4.0

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

#4272 - chore(deps): update biocontainers/isoseq3 docker tag to v3.8.2

Pull Request - State: open - Opened by renovate[bot] about 1 year ago

#4271 - Fix up kallisto

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

#4270 - Update busco

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

#4269 - nf-test interproscan

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

#4268 - Rename utility subworkflows

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

#4267 - Update genomescope

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

#4266 - chore(deps): update biocontainers/htseq docker tag to v2.0.3

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago

#4265 - add agat/convertspgff2tsv module

Pull Request - State: open - Opened by rannick about 1 year ago
Labels: Ready for Review

#4264 - new module: beacon2-ri-tools

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

#4262 - new module: gtfsort

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

#4261 - Add bai as an optionnal output of samtools/merge

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

#4260 - Add panacus histgrowth module

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

#4259 - chore(deps): update biocontainers/goat docker tag to v0.2.5

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago - 1 comment

#4258 - samtools/merge - emit crai file when cram file created

Pull Request - State: closed - Opened by gq1 about 1 year ago

#4255 - chore(config): migrate renovate config

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago

#4254 - Mitohifi channel input

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

#4253 - FEAT: update bclconvert to 4.2.4

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

#4252 - Fix conda declaration

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

#4251 - Add nf-test to centrifuge/centrifuge

Issue - State: open - Opened by koenbossers about 1 year ago
Labels: nf-test

#4250 - add nf-tests and snapshots for kallisto index & quant

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

#4249 - To checksum or not to checksum versions

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

#4248 - Use "error" rather than "exit 1", and removed `quay.io/`

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

#4247 - 3167 new module gridss gridss somatic filter

Pull Request - State: open - Opened by kubranarci about 1 year ago
Labels: Ready for Review

#4246 - Incorrect `BRACKEN_BRACKEN` output session

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

#4245 - change database sufix to nin which is more common in v5 and v4 database

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

#4244 - add samtools to msisensor dependencies

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

#4243 - Update kallistobustools/ref env yml

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

#4242 - arriba/arriba update env

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

#4241 - New module openms/idfilter

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

#4240 - Update seqkit/fx2tab to version 2.5.1

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

#4239 - new module: QUAST/METAQUAST

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

#4238 - pycoqc: add nf-test

Pull Request - State: closed - Opened by koenbossers about 1 year ago
Labels: Ready for Review, nf-test

#4237 - pycoqc: add nf-test

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

#4236 - chore(deps): update biocontainers/glimpse-bio docker tag to v2.0.1

Pull Request - State: open - Opened by renovate[bot] about 1 year ago - 1 comment

#4235 - module `cellranger/multi` has insufficient inputs for antigen analysis

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

#4234 - Give conda environments a name

Issue - State: open - Opened by Emiller88 about 1 year ago - 2 comments

#4233 - new module vcflib/vcfwave

Pull Request - State: open - Opened by nvnieuwk about 1 year ago
Labels: new module, Ready for Review, nf-test

#4232 - Bump MEGAN versions

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

#4231 - Fix linting test not being run for modules with only nf-test tests

Pull Request - State: closed - Opened by nvnieuwk about 1 year ago - 3 comments
Labels: bug, tests, nf-test

#4230 - Allow cat_cat to retain double file extensions for .gz files

Pull Request - State: open - Opened by pmoris about 1 year ago - 1 comment
Labels: bug, enhancement, good first issue, update module, Ready for Review

#4229 - Convert bclconvert and bcl2fastq modules to nf-test

Pull Request - State: closed - Opened by Aratz about 1 year ago
Labels: Ready for Review, nf-test

#4228 - Bump version in MEGAN modules

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

#4227 - new module vcflib/vcfallelicprimitives

Pull Request - State: open - Opened by nvnieuwk about 1 year ago - 2 comments
Labels: new module, Ready for Review, nf-test

#4226 - updated github actions dependencies

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

#4225 - Run prettier on conda envs

Pull Request - State: closed - Opened by Emiller88 about 1 year ago - 4 comments

#4224 - chore(deps): update actions/upload-artifact action to v3

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago

#4223 - chore(deps): update actions/setup-node action to v4

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago

#4222 - chore(deps): update actions/checkout action to v4 - autoclosed

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago

#4219 - chore(deps): update biocontainers/elprep docker tag to v5.1.3

Pull Request - State: open - Opened by renovate[bot] about 1 year ago

#4218 - chore(deps): update biocontainers/das_tool docker tag to v1.1.5

Pull Request - State: open - Opened by renovate[bot] about 1 year ago - 1 comment

#4217 - Renovate nice-to-haves

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

#4216 - Add conda to renovate

Pull Request - State: closed - Opened by Emiller88 about 1 year ago

#4215 - chore(deps): update biocontainers/cutesv docker tag to v2.0.3

Pull Request - State: open - Opened by renovate[bot] about 1 year ago

#4214 - chore(deps): update biocontainers/chromap docker tag to v0.2.5

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago

#4212 - chore(deps): update biocontainers/bowtie2 docker tag to v2.4.5

Pull Request - State: closed - Opened by renovate[bot] about 1 year ago - 1 comment

#4211 - Renovate Dashboard 🤖

Issue - State: open - Opened by renovate[bot] about 1 year ago

#4208 - Sentieon/tnfilter

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

#4207 - 3992 new module openmspeakpickerhires

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

#4206 - Create a workflow to test module multiqc compatibility

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

#4205 - new module: vcflib/vcfallelicprimitives

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

#4204 - proteome_fasta_gz test data added

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

#4203 - *review wanted* New module: Proteinortho

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

#4202 - use custom paths-filter fork

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