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Add support for presupplied annotation files (FAA + GFF or FAA + GBK) #340

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wants to merge 54 commits into from
Closed

Add support for presupplied annotation files (FAA + GFF or FAA + GBK) #340

wants to merge 54 commits into from

Commits on Apr 26, 2023

  1. Start modifying samplesheet check (untested)

    @jfy133
    jfy133 committed Apr 26, 2023
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Commits on May 10, 2023

  1. Made the samplesheet work if columns are existing (python error if th… 

    …e new columns not present)
    @jfy133
    jfy133 committed May 10, 2023
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  2. Continue work

    @jfy133
    jfy133 committed May 10, 2023
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Commits on May 24, 2023

  1. Apply suggestions from code review 

    Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
    @jfy133 @Midnighter
    jfy133 and Midnighter authored May 24, 2023
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  2. Get most of the log working, needs more testing (particularly non FAA… 

    … subwkflws)
    @jfy133
    jfy133 committed May 24, 2023
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Commits on May 31, 2023

  1. Merge branch 'dev' into presupplied-orfs

    @jfy133
    jfy133 authored May 31, 2023
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  2. Sync latest dev changes from annotation into workflow

    @jfy133
    jfy133 committed May 31, 2023
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  3. Update all modules to get right container version and also pyRodigal … 

    …with gzip support
    @jfy133
    jfy133 committed May 31, 2023
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  4. Merge branch 'presupplied-orfs' of github.com:nf-core/funcscan into p… 

    …resupplied-orfs
    @jfy133
    jfy133 committed May 31, 2023
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Commits on Feb 7, 2024

  1. Add test nothing config

    @jfy133
    jfy133 committed Feb 7, 2024
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  2. Merge branch 'dev' into presupplied-orfs

    @jfy133
    jfy133 committed Feb 7, 2024
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  3. Get back to previous starting point before bad merge removed old changes

    @jfy133
    jfy133 committed Feb 7, 2024
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Commits on Feb 14, 2024

  1. Merge branch 'dev' into presupplied-orfs

    @jfy133
    jfy133 committed Feb 14, 2024
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  2. Refactor - have amp/arg working. Includes better fargene tagging

    @jfy133
    jfy133 committed Feb 14, 2024
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  3. Have it working

    @jfy133
    jfy133 committed Feb 14, 2024
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  4. Add test profile and docs

    @jfy133
    jfy133 committed Feb 14, 2024
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  5. Include preanntotaed files in one of the CI runs

    @jfy133
    jfy133 committed Feb 14, 2024
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  6. Fix prettier linting

    @jfy133
    jfy133 committed Feb 14, 2024
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  7. Fix ci command

    @jfy133
    jfy133 committed Feb 14, 2024
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  8. Fix BAKTA to multiqc channel name

    @jfy133
    jfy133 committed Feb 14, 2024
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  9. Add a preannotated test to BGC workflows

    @jfy133
    jfy133 committed Feb 14, 2024
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  10. Make preannotated bgc config accesible

    @jfy133
    jfy133 committed Feb 14, 2024
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  11. Install newer version of antismash to see if it'll work with the GFF … 

    …verison (as reported on antiSMASH github)
    @jfy133
    jfy133 committed Feb 14, 2024
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  12. Use correct dummy files

    @jfy133
    jfy133 committed Feb 14, 2024
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  13. Add warning about Prokka GBK/GFF

    @jfy133
    jfy133 committed Feb 14, 2024
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Commits on Apr 4, 2024

  1. Merge branch 'dev' into presupplied-orfs

    @jasmezz
    jasmezz authored Apr 4, 2024
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  2. Wrapping my head around it

    @jasmezz
    jasmezz committed Apr 4, 2024
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Commits on Apr 5, 2024

  1. Excluded GFF support, fixed multiqc report, update variables etc.

    @jasmezz
    jasmezz committed Apr 5, 2024
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  2. Merge branch 'dev' into presupplied-orfs

    @jasmezz
    jasmezz committed Apr 5, 2024
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  3. Update usage docs and samplesheet

    @jasmezz
    jasmezz committed Apr 5, 2024
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  4. Update modules.config, fix linting, variable typos

    @jasmezz
    jasmezz committed Apr 5, 2024
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Commits on Apr 8, 2024

  1. Fix variable typos, fix multiqc channel for bakta

    @jasmezz
    jasmezz committed Apr 8, 2024
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  2. Fix linting

    @jasmezz
    jasmezz committed Apr 8, 2024
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  3. Prefer pyrodigal in tests, add warning when prodigal + antismash are … 

    …selected.
    @jasmezz
    jasmezz committed Apr 8, 2024
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Commits on Apr 10, 2024

  1. Apply suggestions from code review 

    Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
    @jasmezz @jfy133
    jasmezz and jfy133 authored Apr 10, 2024
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  2. Apply suggestions from code review, fix linting

    @jasmezz
    jasmezz committed Apr 10, 2024
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  3. Change feature to gbk, remove gff from docs

    @jasmezz
    jasmezz committed Apr 10, 2024
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  4. Merge branch 'dev' into presupplied-orfs

    @jasmezz
    jasmezz committed Apr 10, 2024
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  5. Fix "feature" renaming to "gbk"

    @jasmezz
    jasmezz committed Apr 10, 2024
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  6. Fix linting

    @jasmezz
    jasmezz committed Apr 10, 2024
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Commits on Apr 22, 2024

  1. Merge branch 'dev' into presupplied-orfs

    @jasmezz
    jasmezz committed Apr 22, 2024
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  2. Fix variables

    @jasmezz
    jasmezz committed Apr 22, 2024
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Commits on Apr 24, 2024

  1. Fix channels, missing warnin/docs about no splitting for preanno

    @jfy133
    jfy133 committed Apr 24, 2024
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  2. Use correct GBK channel

    @jfy133
    jfy133 committed Apr 24, 2024
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  3. Add log warning when BGC and preannotated input

    @jfy133
    jfy133 committed Apr 24, 2024
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Commits on May 6, 2024

  1. Start trying to fix taxonomy, not working yet as MMSEQS_TAXONOMYDB no… 

    …t executing
    @jfy133
    jfy133 committed May 6, 2024
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Commits on May 15, 2024

  1. Add more GBK/GBFF updates

    @jfy133
    jfy133 committed May 15, 2024
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  2. Remove dumps

    @jfy133
    jfy133 committed May 15, 2024
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  3. Merge branch 'dev' into presupplied-orfs

    @jfy133
    jfy133 committed May 15, 2024
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Commits on May 22, 2024

  1. Only do splitting when BGC workflow executed

    @jfy133
    jfy133 committed May 22, 2024
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  2. Fix taxonomy workflow from possibly getting async between two input c… 

    …hannels for CREATETSV
    @jfy133
    jfy133 committed May 22, 2024
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  3. Fix prokka annotation MQC collection

    @jfy133
    jfy133 committed May 22, 2024
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  4. Fix linting

    @jfy133
    jfy133 committed May 22, 2024
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  5. Make it so deepBGC actually produces otutput, and START send only lon… 

    …g fastas taxonom results to BGC
    @jfy133
    jfy133 committed May 22, 2024
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