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Candidate for 2.0.0 #89

Merged
merged 78 commits into from
Jun 5, 2024
Merged

Candidate for 2.0.0 #89

merged 78 commits into from
Jun 5, 2024

Commits on Apr 22, 2024

  1. Fixed a bug which caused NCBI_FCS_GX to not resume

    @GallVp
    GallVp committed Apr 22, 2024
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  2. Updated modules and sub-workflows

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    GallVp committed Apr 22, 2024
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  3. Template update for nf-core/tools version 2.13.2.dev0

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    GallVp committed Apr 22, 2024
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Commits on Apr 23, 2024

  1. Merged TEMPLATE

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    GallVp committed Apr 23, 2024
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  2. Moved input channel init to sub workflow

    @GallVp
    GallVp committed Apr 23, 2024
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  3. Fixed null versions.yml issue

    @GallVp
    GallVp committed Apr 23, 2024
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  4. Updated modules json

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    GallVp committed Apr 23, 2024
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  5. Updated modules json

    @GallVp
    GallVp committed Apr 23, 2024
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  6. Restored the original version of nf-core/subworkflows/fastq_trim_fast… 

    …p_fastqc
    @GallVp
    GallVp committed Apr 23, 2024
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  7. Fixed linting issues

    @GallVp
    GallVp committed Apr 23, 2024
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  8. Fixed linting issues

    @GallVp
    GallVp committed Apr 23, 2024
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  9. Removed .github/CONTRIBUTING.md from linting

    @GallVp
    GallVp committed Apr 23, 2024
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  10. Now using git URL for nf-core/modules

    @GallVp
    GallVp committed Apr 23, 2024
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  11. Fixed n-core linting

    @GallVp
    GallVp committed Apr 23, 2024
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  12. Template update for nf-core/tools version 2.13.1

    @GallVp
    GallVp committed Apr 23, 2024
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  13. Updated nf-core/template to 2.13.1

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    GallVp committed Apr 23, 2024
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  14. Added pfr/modules key

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    GallVp committed Apr 23, 2024
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  15. Updated linting checks

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    GallVp committed Apr 23, 2024
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  16. Updated tower.yml

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    GallVp committed Apr 23, 2024
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Commits on Apr 29, 2024

  1. Updated LICENSE

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    GallVp committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. Removed release-announcements GitHub workflow and added a list of nf-… 

    …core contributors
    @GallVp
    GallVp committed Apr 30, 2024
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Commits on May 1, 2024

  1. RUNASSEMBLYVISUALIZER is now single threaded for successful execution… 

    … on both Linux and MacOS
    @GallVp
    GallVp committed May 1, 2024
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  2. Added a custom BUNDLELINKS module which respects direction when bundl… 

    …ing dnadiff links
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    GallVp committed May 1, 2024
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Commits on May 2, 2024

  1. Added the ability to create linear synteny plot in addition to the ci… 

    …rcos plot
    @GallVp
    GallVp committed May 2, 2024
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  2. Updated fasta_ltrretriever_lai to fix [ meta, [] ] bug

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    GallVp committed May 2, 2024
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  3. Updated CHANGELOG

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    GallVp committed May 2, 2024
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Commits on May 3, 2024

  1. Fixed java memory overflow issues in RUNASSEMBLYVISUALIZER

    @GallVp
    GallVp committed May 3, 2024
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  2. Updated docs

    @GallVp
    GallVp committed May 3, 2024
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Commits on May 5, 2024

  1. Updated docs

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    GallVp committed May 5, 2024
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Commits on May 6, 2024

  1. Now pipeline can continue if contamination is detected

    @GallVp
    GallVp committed May 6, 2024
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  2. Updated fcs-adaptor to 0.5.0

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    GallVp committed May 6, 2024
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  3. Now fasta ids are sorted in natural order for

    @GallVp
    GallVp committed May 6, 2024
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Commits on May 7, 2024

  1. Added merqury params to schema_input

    @GallVp
    GallVp committed May 7, 2024
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  2. Expanded schema_input

    @GallVp
    GallVp committed May 7, 2024
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Commits on May 8, 2024

  1. Now using FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS for SRA downloads

    @GallVp
    GallVp committed May 8, 2024
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Commits on May 16, 2024

  1. Added MERQURYFK module

    @GallVp
    GallVp committed May 16, 2024
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  2. Template update for nf-core/tools version 2.14.1

    @GallVp
    GallVp committed May 16, 2024
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  3. Updated nf-core/template to 2.14.1

    @GallVp
    GallVp committed May 16, 2024
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  4. Fixed linting issues

    @GallVp
    GallVp committed May 16, 2024
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  5. Updated fasta_explore_search_plot_tidk

    @GallVp
    GallVp committed May 16, 2024
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  6. Replaced GFF3_VALIDATE sub-workflow with GFF3_GT_GFF3_GFF3VALIDATOR_STAT

    @GallVp
    GallVp committed May 16, 2024
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  7. Replaced local BUSCO module with FASTA_GXF_BUSCO_PLOT

    @GallVp
    GallVp committed May 16, 2024
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Commits on May 17, 2024

  1. Replaced local NCBI_FCS_ADAPTOR with nf-core module

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    GallVp committed May 17, 2024
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  2. Added mixed2x test for MERQURY.FK

    @GallVp
    GallVp committed May 17, 2024
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Commits on May 18, 2024

  1. Added module stubs to enable merquryfk in stub test

    @GallVp
    GallVp committed May 18, 2024
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  2. Nowing using a single FETCHNGS workflow to download sra

    @GallVp
    GallVp committed May 18, 2024
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Commits on May 19, 2024

  1. Added phased2x example for merqury.fk analysis

    @GallVp
    GallVp committed May 19, 2024
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Commits on May 21, 2024

  1. Enroute to MERQURY.FK trio mode

    @GallVp
    GallVp committed May 21, 2024
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Commits on May 22, 2024

  1. Migrated to merqury

    @GallVp
    GallVp committed May 22, 2024
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  2. Locally patched MERQURY, MERYL/COUNT and MERYL/UNIONSUM

    @GallVp
    GallVp committed May 22, 2024
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  3. Added stub to merqury

    @GallVp
    GallVp committed May 22, 2024
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  4. Updated docs and removed meryl patches

    @GallVp
    GallVp committed May 22, 2024
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Commits on May 27, 2024

  1. Added plotsr

    @GallVp
    GallVp committed May 27, 2024
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  2. Upgraded locally merqury

    @GallVp
    GallVp committed May 27, 2024
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  3. Fixed merqury/merqury import path

    @GallVp
    GallVp committed May 27, 2024
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  4. Fixed a typo

    @GallVp
    GallVp committed May 27, 2024
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  5. Added JAD labels to tests/stub

    @GallVp
    GallVp committed May 27, 2024
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  6. Now detecting duplicate sequences with SEQKIT/RMDUP

    @GallVp
    GallVp committed May 27, 2024
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Commits on May 28, 2024

  1. Now imported seqkit/rmdup from nf-core/modules

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    GallVp committed May 28, 2024
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  2. Updated modules and sub-workflows

    @GallVp
    GallVp committed May 28, 2024
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  3. Updated usage doc and pfr/params

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    GallVp committed May 28, 2024
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  4. Updated docs

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    GallVp committed May 28, 2024
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  5. Added assembly tag to synteny warning message

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    GallVp committed May 28, 2024
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  6. Updated docs

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    GallVp committed May 28, 2024
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  7. Updated flowchart

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    GallVp committed May 28, 2024
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  8. Fixed a bug in file order for plotsr

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    GallVp committed May 28, 2024
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  9. Set merqury_skip to false in pfr/params

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    GallVp committed May 28, 2024
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Commits on May 30, 2024

  1. Increased time limit for MERQURY_HAPMERS

    @GallVp
    GallVp committed May 30, 2024
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  2. Fixed merqury version reference

    @GallVp
    GallVp committed May 30, 2024
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  3. Disabled legend on dotplot

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    GallVp committed May 30, 2024
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  4. Updated docs

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    GallVp committed May 30, 2024
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  5. Fixed headers in the merqury qv stats table

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    GallVp committed May 30, 2024
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Commits on May 31, 2024

  1. Removed unnecessary ncbi_fcs_gx_tax_id

    @GallVp
    GallVp committed May 31, 2024
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Commits on Jun 3, 2024

  1. Updated fasta_ltrretriever_lai

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    GallVp committed Jun 3, 2024
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  2. Now copying files in NCBI_FCS_GX_SETUP_SAMPLE rather than symlinking … 

    …in an attempt to support NextFlow Fusion
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    GallVp committed Jun 3, 2024
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Commits on Jun 4, 2024

  1. Updated FASTA_LTRRETRIEVER_LAI

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    GallVp committed Jun 4, 2024
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  2. fasta_ltrretriever_lai now supports stub

    @GallVp
    GallVp committed Jun 4, 2024
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  3. Updated docs

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    GallVp committed Jun 4, 2024
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