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DSL2: metagenomics #1019

Merged
merged 164 commits into from
Sep 3, 2024
Merged

DSL2: metagenomics #1019

merged 164 commits into from
Sep 3, 2024

Commits on Mar 29, 2023

  1. partial implementation metagenomicprofiling subwor

    @ilight1542
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  2. 'full' metagenomics profiling implementation

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Commits on Mar 31, 2023

  1. Merge 'ian/dsl2_subworkflow_metagenomics_classification' into dev

    @merszym
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  2. add metagenomics subworkflow

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Commits on Apr 21, 2023

  1. Update nextflow_schema.json 

    from PR review

Co-authored-by: James A. Fellows Yates <[email protected]>
    @ilight1542 @jfy133
    ilight1542 and jfy133 committed Apr 21, 2023
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  2. jfy comments on help text updates

    @ilight1542
    ilight1542 committed Apr 21, 2023
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  3. clarified metagenomics database description

    @ilight1542
    ilight1542 committed Apr 21, 2023
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  4. partial implementation metagenomicprofiling subwor

    @ilight1542
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  5. 'full' metagenomics profiling implementation

    @ilight1542
    ilight1542 committed Apr 21, 2023
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  6. Update nextflow_schema.json 

    from PR review

Co-authored-by: James A. Fellows Yates <[email protected]>
    @ilight1542 @jfy133
    ilight1542 and jfy133 committed Apr 21, 2023
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  7. jfy comments on help text updates

    @ilight1542
    ilight1542 committed Apr 21, 2023
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  8. clarified metagenomics database description

    @ilight1542
    ilight1542 committed Apr 21, 2023
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  9. Merge branch 'dsl2_subworkflow_metagenomics_classification' of https:… 

    …//github.com/ilight1542/eager into dsl2_subworkflow_metagenomics_classification
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  10. updated for nf-core linting

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Commits on Apr 28, 2023

  1. Merge branch 'dsl2-metagenomics' into dsl2_subworkflow_metagenomics_c… 

    …lassification
    @ilight1542
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  2. Merge pull request #971 from ilight1542/dsl2_subworkflow_metagenomics… 

    …_classification

Unify metagenomic implemenations into development dsl2-metagenomics branch

NOTE: still under development
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  3. initial creating of metagenomics_postprocessing

    @ilight1542
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  4. Adjust parameter names

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  5. Fix nextflow schema

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  6. consistency check for postprocessing metagenomics

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  7. partial implem of subwrkflw metagenom_postpr

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  8. Merge branch 'dsl2-metagenomics' of https://github.com/nf-core/eager … 

    …into dsl2-metagenomics
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  9. WIP: Fix metagenomics subworkflow import 

    - WIP: prepare kraken input channel
    @merszym
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  10. updated param name for kraken_save_reads all files

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Commits on May 5, 2023

  1. Complete krakenuniq workflow 

    This commit completes the krakenuniq workflow, tested with the test
profile.
Other classifiers not yet touched!
    @merszym
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  2. partial implementation of krakenparse

    @ilight1542
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  3. Merge Ians Work into mine

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  4. Merge ians and my work (2)

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Commits on May 19, 2023

  1. untested implementation of postprocessing

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Commits on May 26, 2023

  1. Fix paths for subworkflow module import

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  2. modules configuration for ext.args

    @ilight1542
    ilight1542 committed May 26, 2023
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  3. correct filter call in submodule AMPS

    @ilight1542
    ilight1542 committed May 26, 2023
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  4. make kraken_parse.py executable, fix krakenparse.nf module input

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  5. modules.config updating for karken postprocessing

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  6. nextflow config metagenomics_postprocessing

    @ilight1542
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  7. Merge remote-tracking branch 'eager/dsl2-metagenomics' into dsl2-meta… 

    …genomics
    @merszym
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  8. Fix minor typos

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  9. Fix krakenparse args, merge_kraken module+script. Complete Workflow f… 

    …or kraken2
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Commits on Jun 9, 2023

  1. implementation of singlestrnd args into malt: test

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  2. tried to add meta singlestrnd to maltextr input

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Commits on Jun 16, 2023

  1. Fix MALT run with and without malt_group_size 

    In our workflow, database is a channel, not a value, so most of the code didnt work. I remodelled the ch_input_for_malt channel to fit this fact
    @merszym
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  2. make maltextract postprocessing possible

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  3. Krakenuniq workflow done

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Commits on Jun 23, 2023

  1. implementation of metaphlanmerge

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  2. added documentation for metagenomics params

    @ilight1542
    ilight1542 committed Jun 23, 2023
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  3. Fix AMPS output channel names

    @merszym
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  4. Merge 'eager/dsl2-metagenomics' into dsl2-metagenomics

    @merszym
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  5. metaphlan postprocessing implementation updates

    @ilight1542
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  6. Minor schema update

    @merszym
    merszym committed Jun 23, 2023
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  7. Merge branches

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  8. removed unused results channel for metagenomics

    @ilight1542
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  9. Merge branch 'dsl2-metagenomics' of https://github.com/nf-core/eager … 

    …into dsl2-metagenomics
    @ilight1542
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  10. linting fixes

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  11. added metaphlan to readme docs

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  12. streamline maltextract channels

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  13. Merge remote-tracking branch 'eager/dsl2-metagenomics' into dsl2-meta… 

    …genomics
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Commits on Jul 28, 2023

  1. merged dev to metagenomics

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  2. Merge remote-tracking branch 'origin/dev' into dsl2-metagenomics

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  3. fixed metagenomics metaphlan, test runs

    @ilight1542
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Commits on Aug 4, 2023

  1. Tests&Fixes: Krakenextract: uniq prefix, faulty exit condition

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Commits on Aug 7, 2023

  1. metaphlan working

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  2. added prefix to config for metaphlan

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Commits on Aug 9, 2023

  1. Metagenomics: Comprehensive manual tests 

    Added more manual tests to docs/development/manual_tests.md, fixed the
prefix in kraken2
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  2. Test maltextract+AMPS, fix tiny bug in subworkflow, fix publishDir di… 

    …rective
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Commits on Aug 11, 2023

  1. prettier and linting

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  2. Finish tests for MaltExtract

    @merszym
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  3. Merge branch 'dsl2-metagenomics' of github.com:nf-core/eager into dsl… 

    …2-metagenomics
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Commits on Sep 29, 2023

  1. updated gunzip linting

    @ilight1542
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  2. fixed incorrectly named param

    @ilight1542
    ilight1542 committed Sep 29, 2023
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  3. added parameter general combo checks

    @ilight1542
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  4. added parsing of parameter into malt

    @ilight1542
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  5. updated descriptions/help for metagenomics params

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Commits on Oct 6, 2023

  1. hotfix misnamed param

    @ilight1542
    ilight1542 committed Oct 6, 2023
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  2. Fix config typo, add single_end param to metagenomics workflow

    @merszym
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  3. Merge branch 'dsl2-metagenomics' of github.com:nf-core/eager into dsl… 

    …2-metagenomics
    @merszym
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Commits on Oct 20, 2023

  1. updated parameter descriptions, names for clarity

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  2. added parameter checks to top of eager execution

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Commits on Nov 3, 2023

  1. Merge branch 'dev' into dsl2-metagenomics

    @ilight1542
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  2. fixed linting error

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  3. updated documentation for output files

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Commits on Nov 24, 2023

  1. Apply minor suggestions from code review 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @merszym @jfy133
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  2. Minor edits from code-review

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  3. Merge branch 'dsl2-metagenomics' of github.com:nf-core/eager into dsl… 

    …2-metagenomics
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Commits on Dec 1, 2023

  1. minor review suggestions -error calls, param names

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  2. Remove krakenparse+krakenmerge, add taxpasta

    @merszym
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  3. rm duplic of malt_savesamoutput to just savereads

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  4. added gzip for savereads

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  5. Merge 'dsl2-metagenomics' from remote

    @merszym
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  6. linting

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  7. Merge branch 'dsl2-metagenomics' of https://github.com/nf-core/eager … 

    …into dsl2-metagenomics
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Commits on Jan 12, 2024

  1. Remove Metaphlanmergetables, add taxpasta

    @merszym
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  2. Remove unnecessary remnants of taxprofiler code

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  3. include taxpasta also for malt

    @merszym
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Commits on Jan 26, 2024

  1. resolution for malt postprocessing submisison

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  2. updated manual test prep

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Commits on Feb 9, 2024

  1. working outputting of logs

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Commits on Feb 16, 2024

  1. working taxpasta, working maltlog merging

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Commits on Feb 23, 2024

  1. process name prefix fix for cat_cat

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Commits on Mar 18, 2024

  1. Merge pull request #1050 from nf-core/dsl2-malt-testing 

    DSL2: metagenomics testing for malt fixes
    @merszym
    merszym committed Mar 18, 2024
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  2. remove unnecessary .first() declaration from versions channel

    @merszym
    merszym committed Mar 18, 2024
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  3. Ignore AMPS if it fails 

    AMPS fails to create a heatmap and crashes if there are too few numbers of input sequences. There is nothing we can do besides expecting a failure here... Needs to be updated as soon as AMPS is updated
    @merszym
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  4. Run krakenuniq with all samples at once 

    As discussed here #1019 (comment)
    @merszym
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Commits on Mar 19, 2024

  1. fix channel renaming

    @merszym
    merszym committed Mar 19, 2024
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  2. Update MaltExtract module

    @merszym
    merszym committed Mar 19, 2024
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Commits on Mar 20, 2024

  1. WIP: Malt-profiling: Keep strandedness information for malt_group_size 0

    @merszym
    merszym committed Mar 20, 2024
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  2. Run MALT by group_size and strandedness

    @merszym
    merszym committed Mar 20, 2024
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  3. include taxpasta standardise for single sample runs

    @merszym
    merszym committed Mar 20, 2024
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  4. Run maltextract for each malt run

    @merszym
    merszym committed Mar 20, 2024
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  5. Fix grouping of reads by malt_group_size for malt run

    @merszym
    merszym committed Mar 20, 2024
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  6. Code cleanup done

    @merszym
    merszym committed Mar 20, 2024
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  7. Testing: Fix taxpasta merge w/ krakenuniq

    @merszym
    merszym committed Mar 20, 2024
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  8. Merge remote-tracking branch 'eager/dev' into dsl2-metagenomics

    @merszym
    merszym committed Mar 20, 2024
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  9. resolve merge-conflict in manual_test.md

    @merszym
    merszym committed Mar 20, 2024
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  10. Merge branch 'dev' into dsl2-metagenomics

    @merszym
    merszym committed Mar 20, 2024
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  11. Update kraken2 module

    @merszym
    merszym committed Mar 20, 2024
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  12. linting and update nextflow_schema.json

    @merszym
    merszym committed Mar 20, 2024
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  13. Linting again...

    @merszym
    merszym committed Mar 20, 2024
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Commits on Apr 12, 2024

  1. Add kraken2 test-profile, add UNTAR module

    @merszym
    merszym committed Apr 12, 2024
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  2. Apply first suggestions from code review 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @merszym @jfy133
    merszym and jfy133 committed Apr 12, 2024
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  3. (Review) Remove HOST_REMOVAL duplicates

    @merszym
    merszym committed Apr 12, 2024
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  4. Add citations for megan, hops and taxpasta

    @merszym
    merszym committed Apr 12, 2024
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  5. (Review) Remove kraken_parse and kraken_merge scripts

    @merszym
    merszym committed Apr 12, 2024
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  6. Merge branch 'dsl2-metagenomics-review' into dsl2-metagenomics

    @merszym
    merszym committed Apr 12, 2024
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  7. Apply minor suggestions from code review 

    Missed in the first screening

Co-authored-by: James A. Fellows Yates <[email protected]>
    @merszym @jfy133
    merszym and jfy133 committed Apr 12, 2024
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  8. (Review) Apply suggestions from code review

    @merszym
    merszym committed Apr 12, 2024
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Commits on Apr 17, 2024

  1. Merge pull request #1061 from nf-core/dsl2-metagenomics-testprofile-k… 

    …raken

Add kraken2 test-profile, add UNTAR module
    @merszym
    merszym committed Apr 17, 2024
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Commits on Apr 26, 2024

  1. added config for malt testing

    @ilight1542
    ilight1542 committed Apr 26, 2024
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  2. Merge pull request #1062 from nf-core/dsl2-metagenomics-malt-testprofile 

    added config for malt testing
    @merszym
    merszym committed Apr 26, 2024
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  3. Add krakenuniq test profile

    @merszym
    merszym committed Apr 26, 2024
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Commits on May 24, 2024

  1. Add metaphlan testprofile

    @merszym
    merszym committed May 24, 2024
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Commits on Jun 14, 2024

  1. stage input channels in eager subworkflow, not in downstream swfs

    @merszym
    merszym committed Jun 14, 2024
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  2. Skip the maltextract 'results' dir, save directly to process folder

    @merszym
    merszym committed Jun 14, 2024
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Commits on Jun 28, 2024

  1. Fix copy-paste error in bamfiltering module

    @merszym
    merszym committed Jun 28, 2024
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  2. Fix one more bug in bamfilter module

    @merszym
    merszym committed Jun 28, 2024
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  3. resolved PR comments (formating, redundant info)

    @ilight1542
    ilight1542 committed Jun 28, 2024
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  4. last removal of options: text

    @ilight1542
    ilight1542 committed Jun 28, 2024
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  5. Merge branch 'dev' into dsl2-metagenomics

    @ilight1542
    ilight1542 committed Jun 28, 2024
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  6. remove redundant 'single_end = true' statement

    @merszym
    merszym committed Jun 28, 2024
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Commits on Jul 5, 2024

  1. added meta.reference to tool outputs (complexity + kraken2)

    @ilight1542
    ilight1542 committed Jul 5, 2024
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  2. small clarity changes for metagenomics backend

    @ilight1542
    ilight1542 committed Jul 5, 2024
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  3. Fix CI, remove duplicated key in nextflow schema

    @merszym
    merszym committed Jul 5, 2024
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Commits on Jul 19, 2024

  1. applied style and naming changes from PR

    @ilight1542
    ilight1542 committed Jul 19, 2024
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Commits on Aug 9, 2024

  1. Merge 'dev' into 'metagenomics' (bamfilter update)

    @merszym
    merszym committed Aug 9, 2024
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  2. updated test datasets to nf-core/testdatasets eager branch versions

    @ilight1542
    ilight1542 committed Aug 9, 2024
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  3. tmp-fix for wrong module invocation in main WF

    @merszym
    merszym committed Aug 9, 2024
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  4. Merge remote into dsl2-metagenomics

    @merszym
    merszym committed Aug 9, 2024
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  5. added validation catch of nonmerging of PE + metagenomics

    @ilight1542
    ilight1542 committed Aug 9, 2024
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  6. update test-datasets and update withName statements

    @merszym
    merszym committed Aug 9, 2024
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  7. Merge with Ians work

    @merszym
    merszym committed Aug 9, 2024
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Commits on Aug 16, 2024

  1. remove taxpast multiQC channels

    @merszym
    merszym committed Aug 16, 2024
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  2. remove redundant comment

    @merszym
    merszym committed Aug 16, 2024
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  3. Apply minor suggestions from code review 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @merszym @jfy133
    merszym and jfy133 committed Aug 16, 2024
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  4. update docs and fix paths in test configs

    @merszym
    merszym committed Aug 16, 2024
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  5. update docs, include postprocessing in test_configs

    @merszym
    merszym committed Aug 16, 2024
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  6. Update MALT docs, test_config and parameter validation

    @merszym
    merszym committed Aug 16, 2024
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  7. remove defaults from schema help_text entries

    @merszym
    merszym committed Aug 16, 2024
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  8. Apply missed suggestions from code review 

    Co-authored-by: James A. Fellows Yates <[email protected]>
    @merszym @jfy133
    merszym and jfy133 committed Aug 16, 2024
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  9. update the manual tests file

    @merszym
    merszym committed Aug 16, 2024
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  10. Update manual tests, update the docs, fix taxpasta output name

    @merszym
    merszym committed Aug 16, 2024
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  11. Merge branch 'dev' into dsl2-metagenomics

    @merszym
    merszym committed Aug 16, 2024
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  12. fix linting

    @merszym
    merszym committed Aug 16, 2024
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Commits on Sep 2, 2024

  1. Missing sentences

    @jfy133
    jfy133 committed Sep 2, 2024
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  2. Reduce redundant declarations

    @jfy133
    jfy133 committed Sep 2, 2024
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  3. Fix linting

    @jfy133
    jfy133 committed Sep 2, 2024
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