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dsl2 port #182

Closed
wants to merge 78 commits into from
Closed

dsl2 port #182

wants to merge 78 commits into from

Commits on Nov 18, 2020

  1. Try Channel.empty().collect()

    @ewels
    ewels committed Nov 18, 2020
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  2. Try again with various combinations of Channels and collect statements

    @ewels
    ewels committed Nov 18, 2020
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Commits on Nov 19, 2020

  1. Try making CI Nextflow installation logs quieter 

    See nextflow-io/nextflow#1800 (comment)
    @ewels
    ewels committed Nov 19, 2020
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  2. Brackets shouldn't make any difference 

    This code works for ch_multiqc_custom_config - why not here?
    @ewels
    ewels committed Nov 19, 2020
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  3. Fix logic for known_splices in bismark analysis

    @ewels
    ewels committed Nov 19, 2020
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  4. Template update for nf-core/tools version 1.12

    @nf-core-bot
    nf-core-bot committed Nov 19, 2020
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Commits on Dec 3, 2020

  1. Template update for nf-core/tools version 1.12.1

    @nf-core-bot
    nf-core-bot committed Dec 3, 2020
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Commits on Jan 19, 2021

  1. check in required nf-core modules 

    * fastqc
* picard/markduplicates
* preseq/lcextrap
* samtools/flagstat
* samtools/index
* samtools/stats
* samtools/sort
* trimgalore
* multiqc
    @phue
    phue committed Jan 19, 2021
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  2. add required bismark modules 

    * bismark/genome_preparation
* bismark/align
* bismark/deduplicate
* bismark/extract
* bismark/report
* bismark/summary

TODO: write tests and add to nf-core/modules
    @phue
    phue committed Jan 19, 2021
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  3. add required bwameth modules 

    * bwameth/align
* bwameth/index

TODO: write tests and add to nf-core/modules
    @phue
    phue committed Jan 19, 2021
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  4. add required methyldackel modules 

    * methyldackel/extract
* methyldackel/mbias

TODO: write tests and add to nf-core modules
    @phue
    phue committed Jan 19, 2021
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  5. add required qualimap/bamqc module 

    TODO: write tests and add to nf-core/modules
    @phue
    phue committed Jan 19, 2021
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  6. add required samtools/faidx module 

    TODO: write tests and add to nf-core/modules
    @phue
    phue committed Jan 19, 2021
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  7. add functions from nf-core/tools dsl2 template

    @phue
    phue committed Jan 19, 2021
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  8. add samplesheet functionality 

    this is inspired by the functionality in nf-core/nanoseq and
nf-core/rnaseq
The idea is to require a samplesheet to run the pipeline, which will
allow for single/paired end auto-detection and mapping samples against
different reference genomes.

addresses nf-core#181
    @phue
    phue committed Jan 19, 2021
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  9. add bismark subworkflow

    @phue
    phue committed Jan 19, 2021
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  10. add bwameth subworkflow

    @phue
    phue committed Jan 19, 2021
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  11. wire up subworkflows

    @phue
    phue committed Jan 19, 2021
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  12. add file placeholder

    @phue
    phue committed Jan 19, 2021
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  13. update test.config to use samplesheet 

    TODO: needs change in nf-core/test-datasets
    @phue
    phue committed Jan 19, 2021
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  14. update base.config

    @phue
    phue committed Jan 19, 2021
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  15. update igenomes.config 

    baseDir is deprecated
    @phue
    phue committed Jan 19, 2021
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  16. sync some changes from dsl2 template

    @phue
    phue committed Jan 19, 2021
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  17. bump version to 2.0dev

    @phue
    phue committed Jan 19, 2021
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Commits on Feb 11, 2021

  1. Strip brackets

    @ewels
    ewels committed Feb 11, 2021
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  2. Merge remote-tracking branch 'upstream/TEMPLATE' into template-merge-… 

    …1.12.1
    @ewels
    ewels committed Feb 11, 2021
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  3. Merge branch 'template-merge-1.12.1' into known_splices-collect-ifEmpty

    @ewels
    ewels committed Feb 11, 2021
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  4. Remove aws.config

    @ewels
    ewels committed Feb 11, 2021
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  5. Merge pull request nf-core#179 from ewels/known_splices-collect-ifEmpty 

    Template update + fix skipped alignment
    @ewels
    ewels authored Feb 11, 2021
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Commits on Feb 12, 2021

  1. Flesh out changelog

    @ewels
    ewels committed Feb 12, 2021
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  2. Attempt updating all software to latest versions

    @ewels
    ewels committed Feb 12, 2021
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  3. Changelog

    @ewels
    ewels committed Feb 12, 2021
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  4. Downgrade Python and Samtools

    @ewels
    ewels committed Feb 12, 2021
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  5. Be more specific with Python version pin

    @ewels
    ewels committed Feb 12, 2021
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  6. AWS tests - use all aligners, use full scale test profile

    @ewels
    ewels committed Feb 12, 2021
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  7. Clean up README after template merge, add tool citations

    @ewels
    ewels committed Feb 12, 2021
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  8. Fix schema linting failures

    @ewels
    ewels committed Feb 12, 2021
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Commits on Feb 15, 2021

  1. Try downgrading htslib to 1.9 for methyldackl segfault

    @ewels
    ewels committed Feb 15, 2021
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  2. --accel not --accell

    @ewels
    ewels committed Feb 15, 2021
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  3. Env: Remove htslib, downgrade methylseq to 0.4.0

    @ewels
    ewels committed Feb 15, 2021
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Commits on Feb 19, 2021

  1. Merge pull request nf-core#184 from ewels/changelog 

    Flesh out changelog
    @ewels
    ewels authored Feb 19, 2021
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Commits on Feb 20, 2021

  1. Bump MethylDackel back to 0.5.1 for new conda build 

    See dpryan79/MethylDackel#99 (comment)
    @ewels
    ewels committed Feb 20, 2021
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  2. Have a stab at pinning MethylDackel version _and_ build

    @ewels
    ewels committed Feb 20, 2021
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  3. Flesh out changelog

    @ewels
    ewels committed Feb 20, 2021
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  4. Remove duplicate changelog section from PR merges

    @ewels
    ewels committed Feb 20, 2021
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  5. Merge branch 'dev' into software-update

    @ewels
    ewels authored Feb 20, 2021
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  6. Update changelog

    @ewels
    ewels committed Feb 20, 2021
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Commits on Feb 21, 2021

  1. Merge pull request nf-core#185 from ewels/software-update 

    Tidy up lint warnings
    @apeltzer
    apeltzer authored Feb 21, 2021
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Commits on Mar 18, 2021

  1. Template update for nf-core/tools version 1.13

    @nf-core-bot
    nf-core-bot committed Mar 18, 2021
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Commits on Mar 19, 2021

  1. Template update for nf-core/tools version 1.13.1

    @nf-core-bot
    nf-core-bot committed Mar 19, 2021
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Commits on Mar 22, 2021

  1. check in required nf-core modules 

    * fastqc
* picard/markduplicates
* preseq/lcextrap
* samtools/flagstat
* samtools/index
* samtools/stats
* samtools/sort
* trimgalore
* multiqc
    @phue
    phue committed Mar 22, 2021
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  2. add required bismark modules 

    * bismark/genome_preparation
* bismark/align
* bismark/deduplicate
* bismark/extract
* bismark/report
* bismark/summary

TODO: write tests and add to nf-core/modules
    @phue
    phue committed Mar 22, 2021
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  3. add required bwameth modules 

    * bwameth/align
* bwameth/index

TODO: write tests and add to nf-core/modules
    @phue
    phue committed Mar 22, 2021
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  4. add required methyldackel modules 

    * methyldackel/extract
* methyldackel/mbias

TODO: write tests and add to nf-core modules
    @phue
    phue committed Mar 22, 2021
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  5. add required qualimap/bamqc module 

    TODO: write tests and add to nf-core/modules
    @phue
    phue committed Mar 22, 2021
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  6. add required samtools/faidx module 

    TODO: write tests and add to nf-core/modules
    @phue
    phue committed Mar 22, 2021
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  7. add functions from nf-core/tools dsl2 template

    @phue
    phue committed Mar 22, 2021
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  8. add samplesheet functionality 

    this is inspired by the functionality in nf-core/nanoseq and
nf-core/rnaseq
The idea is to require a samplesheet to run the pipeline, which will
allow for single/paired end auto-detection and mapping samples against
different reference genomes.

addresses nf-core#181
    @phue
    phue committed Mar 22, 2021
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  9. add bismark subworkflow

    @phue
    phue committed Mar 22, 2021
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  10. add bwameth subworkflow

    @phue
    phue committed Mar 22, 2021
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  11. Merge dev

    @phue
    phue committed Mar 22, 2021
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  12. add file placeholder

    @phue
    phue committed Mar 22, 2021
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  13. update test.config to use samplesheet 

    TODO: needs change in nf-core/test-datasets
    @phue
    phue committed Mar 22, 2021
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  14. update base.config

    @phue
    phue committed Mar 22, 2021
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  15. sync some changes from dsl2 template

    @phue
    phue committed Mar 22, 2021
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  16. bump version to 2.0dev

    @phue
    phue committed Mar 22, 2021
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  17. update test profile for dsl2 

    the pipeline now requires a samplesheet
    @phue
    phue committed Mar 22, 2021
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  18. remove files that become obsolete with dsl2

    @phue
    phue committed Mar 22, 2021
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  19. Merge branch 'dsl2' of https://github.com/phue/methylseq into dsl2

    @phue
    phue committed Mar 22, 2021
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  20. update ci.yml 

    remove conda and docker related actions
    @phue
    phue committed Mar 22, 2021
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  21. update nextflow.config

    @phue
    phue committed Mar 22, 2021
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Commits on Mar 23, 2021

  1. prepare for sync with nf-core/modules

    @phue
    phue committed Mar 23, 2021
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  2. Template update for nf-core/tools version 1.14.dev0

    @phue
    phue committed Mar 23, 2021
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  3. Merge branch 'TEMPLATE' into dsl2 

    merging dsl2-template
    @phue
    phue committed Mar 23, 2021
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  4. sync with nf-core/modules

    @phue
    phue committed Mar 23, 2021
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Commits on Mar 24, 2021

  1. cleanup some duplicated files

    @phue
    phue committed Mar 24, 2021
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  2. finish restructuring; create local modules where needed

    @phue
    phue committed Mar 24, 2021
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  3. update nextflow_schema.json

    @phue
    phue committed Mar 24, 2021
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