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Dev -> Master for 1.1.0 release #86

Merged
merged 80 commits into from
Jan 23, 2023
Merged

Dev -> Master for 1.1.0 release #86

merged 80 commits into from
Jan 23, 2023

Commits on Oct 12, 2022

  1. replace local demultiplex subwf with nf-core one

    @matthdsm
    matthdsm committed Oct 12, 2022
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  2. drop input_check.nf, fixes #52

    @matthdsm
    matthdsm committed Oct 12, 2022
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  3. bump bases2fastq module

    @matthdsm
    matthdsm committed Oct 12, 2022
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  4. WIP, add bases2fastq subworkflow

    @matthdsm
    matthdsm committed Oct 12, 2022
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  5. control demultiplexer selection with switch

    @matthdsm
    matthdsm committed Oct 12, 2022
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  6. bugfix

    @matthdsm
    matthdsm committed Oct 12, 2022
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  7. add docs for bases2fastq fq header

    @matthdsm
    matthdsm committed Oct 12, 2022
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  8. use b2fq subwf

    @matthdsm
    matthdsm committed Oct 12, 2022
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  9. bugfix

    @matthdsm
    matthdsm committed Oct 12, 2022
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  10. add @Midnighter's FormattingService to pretty dump some logs

    @matthdsm
    matthdsm committed Oct 12, 2022
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  11. b2fq: fix samplename regex

    @matthdsm
    matthdsm committed Oct 12, 2022
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Commits on Oct 13, 2022

  1. kill fastqc, long live falco; fixes #62

    @matthdsm
    matthdsm committed Oct 13, 2022
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  2. fix MQC report, fixes #64

    @matthdsm
    matthdsm committed Oct 13, 2022
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  3. Update Citations [skip_ci]

    @matthdsm
    matthdsm committed Oct 13, 2022
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  4. update outputs [skip_ci]

    @matthdsm
    matthdsm committed Oct 13, 2022
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  5. add subway map

    @nvnieuwk
    nvnieuwk committed Oct 13, 2022
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  6. update changelog [skip_ci]

    @matthdsm
    matthdsm committed Oct 13, 2022
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  7. update readme [skip_ci]

    @matthdsm
    matthdsm committed Oct 13, 2022
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  8. prettier

    @nvnieuwk
    nvnieuwk committed Oct 13, 2022
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  9. Merge pull request #66 from nvnieuwk/subway-map 

    add subway map
    @matthdsm
    matthdsm authored Oct 13, 2022
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  10. add subway map

    @nvnieuwk @matthdsm
    nvnieuwk authored and matthdsm committed Oct 13, 2022
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  11. prettier

    @nvnieuwk @matthdsm
    nvnieuwk authored and matthdsm committed Oct 13, 2022
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  12. [skip_ci] update changelog

    @matthdsm
    matthdsm committed Oct 13, 2022
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  13. Merge pull request #63 from nf-core/feature/nf-core_subworkflows 

    Workflow updates
    @matthdsm
    matthdsm authored Oct 13, 2022
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Commits on Oct 20, 2022

  1. fix: Uncomment pipeline-specific instititutional configs

    @edmundmiller
    edmundmiller committed Oct 20, 2022
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  2. chore: Update CHANGELOG

    @edmundmiller
    edmundmiller committed Oct 20, 2022
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  3. Merge pull request #67 from nf-core/instititutional-configs 

    Enable instititutional configs
    @drpatelh
    drpatelh authored Oct 20, 2022
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Commits on Oct 21, 2022

  1. add wf qc options

    @matthdsm
    matthdsm committed Oct 21, 2022
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  2. fix fastq output, update markdowns

    @matthdsm
    matthdsm committed Oct 21, 2022
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  3. update schema

    @matthdsm
    matthdsm committed Oct 21, 2022
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  4. prettier

    @matthdsm
    matthdsm committed Oct 21, 2022
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  5. typos

    @matthdsm
    matthdsm committed Oct 21, 2022
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  6. feat(bases2fastq): Apply trimming if trim_fastq

    @edmundmiller
    edmundmiller committed Oct 21, 2022
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Commits on Oct 24, 2022

  1. change in config to if in workflow

    @matthdsm
    matthdsm committed Oct 24, 2022
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Commits on Nov 4, 2022

  1. fix wf errors

    @matthdsm
    matthdsm committed Nov 4, 2022
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  2. nfcore linting

    @matthdsm
    matthdsm committed Nov 4, 2022
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  3. bump fastp module

    @matthdsm
    matthdsm committed Nov 4, 2022
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Commits on Nov 23, 2022

  1. Merge pull request #70 from nf-core/feat/wf_qc_options 

    Feat/wf qc options
    @edmundmiller
    edmundmiller authored Nov 23, 2022
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Commits on Nov 24, 2022

  1. build: Run nf-test init

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  2. test(bclconvert): Add initial test

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  3. test(bases2fastq): Add initial test

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  4. test(bcl2fastq): Add initial test

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  5. chore: Update CHANGELOG

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  6. chore: Make CHANGELOG consistant

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  7. ci: Yoink pipeline from fetchngs

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  8. docs: Add nf-test badge to README

    @edmundmiller
    edmundmiller committed Nov 24, 2022
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  9. Merge pull request #73 from nf-core/nf-test 

    nf-test init
    @edmundmiller
    edmundmiller authored Nov 24, 2022
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Commits on Nov 29, 2022

  1. bump version number

    @matthdsm @edmundmiller
    matthdsm authored and edmundmiller committed Nov 29, 2022
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  2. update dump tags

    @matthdsm @edmundmiller
    matthdsm authored and edmundmiller committed Nov 29, 2022
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  3. overhaul input parsing

    @matthdsm @edmundmiller
    matthdsm authored and edmundmiller committed Nov 29, 2022
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  4. test: Run nf-test generate function

    @edmundmiller
    edmundmiller committed Nov 29, 2022
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  5. test: Comment out future tests

    @edmundmiller
    edmundmiller committed Nov 29, 2022
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  6. style: Fix comment indent

    @edmundmiller
    edmundmiller committed Nov 29, 2022
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  7. test: Function fails for extract_csv

    @edmundmiller
    edmundmiller committed Nov 29, 2022
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Commits on Nov 30, 2022

  1. Merge pull request #75 from nf-core/feat/update_input_parsing 

    Feat/update input parsing
    @matthdsm
    matthdsm authored Nov 30, 2022
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Commits on Dec 5, 2022

  1. chore: Highlight test files

    @edmundmiller
    edmundmiller committed Dec 5, 2022
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Commits on Dec 6, 2022

  1. Merge pull request #76 from nf-core/highlist-test-files 

    Highlight test files
    @edmundmiller
    edmundmiller authored Dec 6, 2022
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Commits on Dec 8, 2022

  1. Template update for nf-core/tools version 2.7.1

    @nf-core-bot
    nf-core-bot committed Dec 8, 2022
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Commits on Dec 19, 2022

  1. Template update for nf-core/tools version 2.7.2

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    nf-core-bot committed Dec 19, 2022
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Commits on Jan 18, 2023

  1. fixed if statements for skip_tools

    @glichtenstein
    glichtenstein committed Jan 18, 2023
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  2. fix(#82): Use correct fastp output

    @edmundmiller
    edmundmiller committed Jan 18, 2023
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Commits on Jan 19, 2023

  1. test: Update tests 

    Should have been addressed in #70
    @edmundmiller
    edmundmiller committed Jan 19, 2023
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  2. test(#82): Add test to skip trimming

    @edmundmiller
    edmundmiller committed Jan 19, 2023
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  3. test(#82): Add test for skipping fastp

    @edmundmiller
    edmundmiller committed Jan 19, 2023
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  4. test(#82): Add test to skip both fastp and fastqc

    @edmundmiller
    edmundmiller committed Jan 19, 2023
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  5. test(#82): Test only skipping fastqc

    @edmundmiller
    edmundmiller committed Jan 19, 2023
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  6. chore: Update CHANGELOG

    @edmundmiller
    edmundmiller committed Jan 19, 2023
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  7. Merge pull request #83 from glichtenstein/bug/fixed-if-statements-for… 

    …-skip-tools

By default fastp and falco are always skipped even without providing skip_tools options. After this change, skip_tools worked as expected i.e: --skip_tools fastp.

However there is still a problem with --trim_fastq true

No such variable: Exception evaluating property 'fastq' for nextflow.script.ChannelOut, Reason: groovy.lang.MissingPropertyException: No such property: fastq for class: groovyx.gpars.dataflow.DataflowBroadcast
 -- Check script './workflows/demultiplex.nf' at line: 155

Problematic lines

 if (trim_fastq) {
                ch_fastq_to_qc = FASTP.out.fastq
            }

This closes #82
    @edmundmiller
    edmundmiller committed Jan 19, 2023
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Commits on Jan 20, 2023

  1. Merge branch 'dev' into nf-core-template-merge-2.7.2

    @edmundmiller
    edmundmiller committed Jan 20, 2023
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  2. chore: Add new nextflow version to CHANGELOG

    @edmundmiller
    edmundmiller committed Jan 20, 2023
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  3. chore: Bump modules 

    nf-core modules update
    @edmundmiller
    edmundmiller committed Jan 20, 2023
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  4. chore: Update CHANGELOG

    @edmundmiller
    edmundmiller committed Jan 20, 2023
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  5. Merge pull request #78 from nf-core/nf-core-template-merge-2.7.2 

    Important! Template update for nf-core/tools v2.7.2
    @edmundmiller
    edmundmiller authored Jan 20, 2023
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  6. chore: Add DOI

    @edmundmiller
    edmundmiller committed Jan 20, 2023
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  7. style: Turn contributors into a list

    @edmundmiller
    edmundmiller committed Jan 20, 2023
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  8. docs: Update link to samplesheet 

    closes #79
    @edmundmiller
    edmundmiller committed Jan 20, 2023
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Commits on Jan 23, 2023

  1. fix: Shortern doi 

    Also adds two blank lines
    @edmundmiller
    edmundmiller committed Jan 23, 2023
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  2. chore: Add attributions to CHANGELOG 

    nf-core/website#1551
    @edmundmiller
    edmundmiller committed Jan 23, 2023
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  3. test: Remove commented out code

    @edmundmiller
    edmundmiller committed Jan 23, 2023
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  4. chore: Bump version

    @edmundmiller
    edmundmiller committed Jan 23, 2023
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