nf-core/methylseq issues and pull requests

#359 - Fix expansion of ignore_r1 parameters in modules.config

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

#358 - Parameters ignore_r1 for methylationextractor not expanded

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

#357 - fix for bug #354 - dev branch

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

#356 - post-release dev bump version and snapshots

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

#355 - fix for bug #354

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

#354 - methylKit-compatible files are not copied to publishDir

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

#353 - Error when providing a bwameth index (MethylSeq v2.4.0 and v2.5.0)

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

#352 - methylseq - bwameth index failure, pipeline does't run, but bismark does

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

#351 - Pipeline unable to recognise samples processed across multiple lanes

Issue - State: open - Opened by jma1991 about 1 year ago
Labels: bug

#350 - Add scatter CI

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

#349 - pipeline improvements

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

#348 - Release Prep for 2.5.0

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

#347 - Dev -> Master 2.5.0

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

#346 - Citationtools

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

#345 - Maintainers

Pull Request - State: closed - Opened by Emiller88 about 1 year ago - 2 comments

#344 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 1 comment

#343 - Support pipeline-specific configs

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

#342 - Add exists to Schema

Pull Request - State: closed - Opened by Emiller88 about 1 year ago - 2 comments

#341 - Use fromSamplesheet

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

#339 - nf-validation

Issue - State: closed - Opened by Emiller88 over 1 year ago
Labels: enhancement

#338 - Refactor kit processing to be maintainable

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

#337 - Add exists to schema

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#336 - Update toolCitationText

Issue - State: closed - Opened by Emiller88 over 1 year ago - 1 comment

#335 - Wrong display values for "zymo" and "em_seq" presets on help page

Pull Request - State: closed - Opened by wassimsalam01 over 1 year ago - 4 comments
Labels: bug

#334 - test failure

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

#333 - Apply easy module updates

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

#332 - methylseq is requesting very high compute resources I don't have.

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

#331 - Publish coverage files

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

#330 - Leave spare memory for samtools sort (again)

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

#329 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#328 - `samtools sort` overwrites

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

#327 - Add `--skip_fastqc` option

Issue - State: open - Opened by bounlu over 1 year ago
Labels: enhancement

#326 - bump version 2.5.0dev

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

#325 - fix ignore params help text [ci skip]

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

#324 - CI-update-skip-dev-condition, update README and changelog

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

#323 - ci: Attempt to remove duplicate code

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

#322 - 2.4.0 code review fixes

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

#321 - Dev -> Master 2.4.0

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

#320 - bump version 2.4.0

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

#319 - bump-version 2.4.0

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

#318 - disable CI PR commenter

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

#317 - removed unused directory

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

#316 - 303-add-bamqc-regions-file-param

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

#315 - Fix/maintenance fixes

Pull Request - State: closed - Opened by sateeshperi over 1 year ago - 14 comments

#314 - Update nextflow.config

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

#313 - Hs metrics

Pull Request - State: open - Opened by RogerHw over 1 year ago - 5 comments
Labels: WIP

#312 - CI-add-pr-comment-if-logic

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

#311 - Add bismark --ignore and --ignore_3prime options

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

#310 - bump-nf-tests-snapshots-2.8.0

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

#309 - Something ain't right with that template...

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: bug

#308 - set-default-registry-docker-podman

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

#307 - prepare-genome-value-channels

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

#306 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago

#305 - Empty .fasta file at beginning of Bismark alignment

Issue - State: open - Opened by PatrickMaclean over 1 year ago - 10 comments
Labels: bug

#304 - update-modules-snapshots

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

#303 - Add --bamqc_regions_file parameter

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

#302 - Regions file parameter for Qualimap Bamqc

Issue - State: closed - Opened by berguner over 1 year ago
Labels: enhancement

#301 - Use nf-test tags

Issue - State: open - Opened by Emiller88 over 1 year ago
Labels: enhancement

#300 - Fix/update nf tests

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

#299 - --ignore_r2 and --ignore_3prime_R2 are not working as intended

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

#298 - remove unused output folder

Pull Request - State: closed - Opened by njspix almost 2 years ago

#297 - stranded_CpG_report folder is empty

Issue - State: closed - Opened by liuyangzzu almost 2 years ago - 4 comments
Labels: bug

#296 - Run tests on changes

Pull Request - State: closed - Opened by Emiller88 almost 2 years ago - 2 comments

#295 - Add Biscuit

Pull Request - State: open - Opened by njspix almost 2 years ago - 5 comments
Labels: WIP

#294 - Remove fast fail

Pull Request - State: closed - Opened by Emiller88 almost 2 years ago - 3 comments

#293 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 4 comments

#292 - Bump v2.4.0dev

Pull Request - State: closed - Opened by ewels almost 2 years ago

#291 - Remove .ifEmpty(null)

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#290 - Bump to v2.3.0 in changelog and config

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#289 - Dev -> Master for release

Pull Request - State: closed - Opened by ewels almost 2 years ago - 3 comments

#288 - Tools 2.7.1 merge

Pull Request - State: closed - Opened by ewels almost 2 years ago - 4 comments

#287 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago

#286 - First attempt at fetching test data before running nf-test

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#285 - Add config for longer timeouts on Bismark + bwameth alignment processes

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#284 - Samplesheet extra logging

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#283 - Additional downstream processes written in DSL1 -- UPGRADE now to DSL2

Issue - State: open - Opened by Jani-94 almost 2 years ago - 1 comment
Labels: enhancement

#282 - Refactor subworkflows

Pull Request - State: closed - Opened by ewels almost 2 years ago - 3 comments

#281 - Add a `tower.yml` file to enable Reports in Nextflow Tower

Pull Request - State: closed - Opened by ewels almost 2 years ago - 3 comments

#280 - Wrap `params.fasta` with `file()` when used in processes.

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#279 - Fix nf-test

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#278 - Get to the bottom of index tests

Issue - State: closed - Opened by Emiller88 almost 2 years ago - 2 comments

#277 - Bump v2.3.0dev

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#276 - Dev -> Master for v2.2.0 release

Pull Request - State: closed - Opened by ewels almost 2 years ago - 1 comment

#275 - Bump to v2.2.0 for release

Pull Request - State: closed - Opened by ewels almost 2 years ago

#274 - `--genome` in bwameth and bismark DOESN’T work in v2.1.0

Issue - State: closed - Opened by PanZiwei almost 2 years ago - 1 comment
Labels: bug

#273 - Fixed Bismark and bwa-meth index locations

Pull Request - State: closed - Opened by FelixKrueger about 2 years ago - 1 comment

#272 - 238 add ability to merge fastqs

Pull Request - State: closed - Opened by SpikyClip about 2 years ago - 2 comments

#271 - Sort out `--cytosine_report`

Issue - State: closed - Opened by ewels about 2 years ago - 1 comment

#270 - Remove orphaned `*per_multicore` params.

Pull Request - State: closed - Opened by ewels about 2 years ago - 1 comment

#269 - fix params typo

Pull Request - State: closed - Opened by ewels about 2 years ago - 1 comment

#268 - Update bismark/summary module

Pull Request - State: closed - Opened by ewels about 2 years ago - 1 comment

#267 - Bump version

Pull Request - State: closed - Opened by ewels about 2 years ago - 1 comment

#266 - v2.1.0 release.

Pull Request - State: closed - Opened by ewels about 2 years ago - 2 comments

#265 - Bump to 2.1.0

Pull Request - State: closed - Opened by ewels about 2 years ago - 1 comment

#264 - Bismark input params for `--multicore` are not used

Issue - State: closed - Opened by bounlu about 2 years ago - 1 comment
Labels: bug

#263 - Typo ?

Issue - State: closed - Opened by bounlu about 2 years ago - 1 comment
Labels: bug

GitHub / nf-core/methylseq issues and pull requests