Code

dsl2 port#199

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ewels merged 191 commits intodevnf-core/methylseq:devfrom dsl2nf-core/methylseq:dsl2Copy head branch name to clipboardNov 3, 2022

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Commits

Commits on Jan 19, 2021

• check in required nf-core modules

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• add required bismark modules

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• add required bwameth modules

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• add required methyldackel modules

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• add required qualimap/bamqc module

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• add required samtools/faidx module

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• add functions from nf-core/tools dsl2 template

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• add samplesheet functionality

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• add bismark subworkflow

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• add bwameth subworkflow

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• wire up subworkflows

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• add file placeholder

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• update test.config to use samplesheet

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• update base.config

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• update igenomes.config

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• sync some changes from dsl2 template

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• bump version to 2.0dev

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Commits on Mar 22, 2021

• check in required nf-core modules

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• add required bismark modules

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• add required bwameth modules

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• add required methyldackel modules

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• add required qualimap/bamqc module

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• add required samtools/faidx module

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• add functions from nf-core/tools dsl2 template

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• add samplesheet functionality

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• add bismark subworkflow

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• add bwameth subworkflow

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• Merge dev

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• add file placeholder

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• update test.config to use samplesheet

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• update base.config

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• sync some changes from dsl2 template

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• bump version to 2.0dev

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• update test profile for dsl2

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• remove files that become obsolete with dsl2

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• Merge branch 'dsl2' of https://github.com/phue/methylseq into dsl2

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• update ci.yml

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• update nextflow.config

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Commits on Mar 23, 2021

• prepare for sync with nf-core/modules

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• Template update for nf-core/tools version 1.14.dev0

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• Merge branch 'TEMPLATE' into dsl2

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• sync with nf-core/modules

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Commits on Mar 24, 2021

• cleanup some duplicated files

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• finish restructuring; create local modules where needed

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• update nextflow_schema.json

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Commits on Mar 25, 2021

• enable tests for dsl2 branch

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Commits on Mar 29, 2021

• fix conda and podman profiles

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• remove duplicated section in README

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• fix bismark/align argument parsing

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• improve handling of iGenomes indices

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• bismark workflow: only publish sorted bam file

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Commits on Apr 3, 2021

• bismark/report: allow skipping of read deduplication

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• bismark/summary improve matching of process output

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• methyldackel: fix version scraping

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• fix issue leading to missing data in multiqc report

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Commits on Apr 4, 2021

• Merge remote-tracking branch 'origin/dev' into dsl2

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• minor cleanup

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• cleanup groovy libs

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• bump bwameth container build to match conda version

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Commits on Apr 6, 2021

• lint with nf 21.03.0-edge

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• update .nf-core-lint.yaml

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• update .nf-core-lint.yaml

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Commits on Apr 8, 2021

• update test profiles

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Commits on Jun 24, 2021

• Manually fix merge conflicts

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• Bring bwameth fix from DSL1 into DSL2 module

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• Try removing some of the nf-core linting ignores

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• Don't pin Nextflow version in linting.yml

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• Update lib/NfcoreSchema.groovy to template version, update .nf-core-lint.yml

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Commits on Jul 13, 2021

• Template update for nf-core/tools version 2.0

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• Template update for nf-core/tools version 2.0.1

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Commits on Jul 27, 2021

• Template update for nf-core/tools version 2.1

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Commits on Nov 4, 2021

• Update .nf-core-lint.yaml

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Commits on Dec 14, 2021

• Template update for nf-core/tools version 2.2

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Commits on Mar 15, 2022

• Template update for nf-core/tools version 2.3

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Commits on Mar 16, 2022

• Template update for nf-core/tools version 2.3.dev0

  

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Commits on Mar 17, 2022

• Merge branch 'TEMPLATE' into dsl2; rough commit

  njspix

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• update modules

  njspix

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• more minor tweaks to get lint at least running

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• CLI updates

  

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• remove duplicates in schema

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Commits on Mar 18, 2022

• update check_samplesheet to make genome optional

  njspix

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• more updates for optional --genome

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• make --genome or --fasta input optional

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Commits on Mar 23, 2022

• Template update for nf-core/tools version 2.3.1

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Commits on Mar 24, 2022

• Template update for nf-core/tools version 2.3.2

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Commits on Mar 31, 2022

• trying to get new plumbing working

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• got plumbing working through fastqc (!)

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Commits on Apr 1, 2022

• try to get executable bits right

  

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• Template update for nf-core/tools version 2.3.2

  

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• merge latest template; revert samplesheet py

  

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• update modules

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• alignment plumbing seems ok

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• plumbing seems to be working all the way through

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• put fasta back in test config

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Commits on Apr 4, 2022

• prettier

  

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• try to fix a few lint errors

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Commits on Apr 7, 2022

• more updates...

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• plumbing seems to be working for bwameth now

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Commits on Apr 8, 2022

• formatting

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Commits on Apr 25, 2022

• fix editorconfig

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• fix linting but broke ci tests

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• prettier

  

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Commits on Apr 26, 2022

• update modules

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• run prettier

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• add test_paired

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• clean up 'no process matching config' warnings

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• remove unused modules

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• Merge pull request #230 from njspix/dsl2

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Commits on May 10, 2022

• try to publish bams

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• publishDir changes

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• more publish fixes

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• another publishdir fix

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Commits on May 16, 2022

• Template update for nf-core/tools version 2.4

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Commits on May 18, 2022

• few more publish alterations

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• update modules

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• fix a few linting errors

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• run prettier

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• update picard_markdup to long syntax

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Commits on May 19, 2022

• lint

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• Template update for nf-core/tools version 2.4.1

  

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• Merge branch 'TEMPLATE' into dsl2

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• add gcref params for qualimap

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• change plumbing for bismark to sort before dedup

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• change bismark output channel

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• update config andschema

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• preemptive change to bismark

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• syntax and prettier

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• make schema lint happy

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• add fasta param back in

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• fix config problems

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• add enable_conda to schema

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• prettier

  

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Commits on May 20, 2022

• revert to nf-core bismark/methylationextractor

  

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• bismark/methextract pe-specific args in config

  

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• closure for querying meta in config

  

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• remove flag from test profile

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Commits on May 25, 2022

• remove functions.nf

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Commits on Jun 27, 2022

• allow specify genome with --genome

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Commits on Jun 28, 2022

• Revert "change plumbing for bismark to sort before dedup"

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• fix plumbing for sorting

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Commits on Jul 1, 2022

• add nextseq trimming option

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• add nextseq_trim option and update schema

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Commits on Jul 7, 2022

• change nextseq_trim defaults

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Commits on Aug 30, 2022

• Template update for nf-core/tools version 2.5

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Commits on Sep 1, 2022

• Template update for nf-core/tools version 2.5.1

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Commits on Sep 14, 2022

• Merge branch 'nf-core-template-merge-2.5.1' into dsl2

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• Fix CI workflows

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• Remove .vscode

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• Merge pull request #244 from ewels/dsl2

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• Update modules.json to new format

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• Updated all modules to latest versions

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• Removed unused get_software_versions.nf local module

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• Tidy up CITATIONS.md

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• Add pipeline Zenodo DOI to lib and citations.

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• Remove old lib files

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Commits on Sep 15, 2022

• Update MultiQC and fix channels

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• Make nextflow.config match the template as much as possible

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Commits on Sep 16, 2022

• Merge pull request #245 from ewels/dsl2

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Commits on Sep 27, 2022

• Merge pull request #246 from ewels/dsl2_remove_lib

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Commits on Sep 28, 2022

• Update modules

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• Add label and when condition to samplesheet_check local module

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• Merge pull request #247 from ewels/dsl2

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Commits on Oct 4, 2022

• Template update for nf-core/tools version 2.6

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Commits on Nov 2, 2022

• Update modules.json to new format

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• Moved modules up a directory for restructuring

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• Update modules import paths

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• Reset accidentally broken modules.json

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• Update modules

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• Manually update nextflow config, schema and workflow for template update

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• Tools v2.6 template update - fix merge conflicts

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• Remove duplication of ch_multiqc_custom_config

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• Add fasta and fai to Picard markdups

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• Remove unused BISMARK_INDEX modules config

  ewels

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• Add fasta_index, bismark_index and bwa_meth_index params back again

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• Couple of code comments

  ewels

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• Ditch ch_ prefixes

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• Remove methods description TODO prompt

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• Alias both samtools_sort processes with different names

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• Add the reference genome index path back to the CI

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• Use file() on supplied reference paths

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• Refactor version collection in subworkflows

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• Emit versions, not ch_versions

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• Ok use versions not ch_versions EVERYWHERE

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• Update CI: BWA-meth takes index as a directory now, not a stub path.

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Commits on Nov 3, 2022

• Correct paths to previously generated indices in CI tests

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• Need to go to bed..

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• Merge pull request #249 from ewels/dsl2

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• Update methylkit/extract module.

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• Add some extra pipeline flags on the second CI test run

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• Merge pull request #250 from ewels/dsl2

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• CI tests: Use -resume to speed things along

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