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change input type for finish_asm #9

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change input type for finish_asm #9

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Commits on Dec 7, 2022

  1. change input type for finish_asm

    @scanon
    scanon committed Dec 7, 2022
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Commits on Jan 28, 2023

  1. add make_info_file task

    Chienchi Lo committed Jan 28, 2023
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  2. udpate README

    Chienchi Lo committed Jan 28, 2023
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  3. fix missing make_info file direct

    Chienchi Lo committed Jan 28, 2023
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Commits on Jun 10, 2023

  1. Merge pull request #11 from microbiomedata/make_info 

    Werkflow to master for ASM
    @scanon
    scanon authored Jun 10, 2023
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Commits on Jul 3, 2023

  1. added release workflow for assembly

    Michal-Babins committed Jul 3, 2023
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  2. switched out uses for run

    Michal-Babins committed Jul 3, 2023
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  3. removed v from version bump

    Michal-Babins committed Jul 3, 2023
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Commits on Jul 6, 2023

  1. removed unused variables

    Michal-Babins committed Jul 6, 2023
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Commits on Jul 10, 2023

  1. added version.txt and upated create_release.yml to source from versio… 

    …n.txt
    Michal-Babins committed Jul 10, 2023
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Commits on Jul 14, 2023

  1. remove unused input_file variable from finish_asm

    Michal-Babins committed Jul 14, 2023
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Commits on Oct 17, 2023

  1. add jgi_meta_wdl submodules

    Chienchi Lo committed Oct 17, 2023
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Commits on Oct 19, 2023

  1. changed wdl files to version 1.0

    @kaijli
    kaijli committed Oct 19, 2023
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Commits on Nov 3, 2023

  1. update jgi_meta_wdl submodules

    Chienchi Lo committed Nov 3, 2023
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Commits on Nov 7, 2023

  1. quick script to choose between long and short reads

    @kaijli
    kaijli committed Nov 7, 2023
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Commits on Nov 9, 2023

  1. take one input either to long reads workflow or to short reads workflow

    Chienchi Lo committed Nov 9, 2023
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Commits on Nov 12, 2023

  1. working on input dependencies

    @kaijli
    kaijli committed Nov 12, 2023
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  2. merged to include interleave

    @kaijli
    kaijli committed Nov 12, 2023
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  3. having trouble importing jgi long reads

    @kaijli
    kaijli committed Nov 12, 2023
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  4. quick json to test choice wdl

    @kaijli
    kaijli committed Nov 12, 2023
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Commits on Nov 13, 2023

  1. update jgi_meta_wdl submodules

    Chienchi Lo committed Nov 13, 2023
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  2. move make_interleaved_reads into shortReads condition, and add contai… 

    …ner in interleaved_reads.wdl
    Chienchi Lo committed Nov 13, 2023
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Commits on Nov 14, 2023

  1. working on file localization errors

    @kaijli
    kaijli committed Nov 14, 2023
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  2. added imports.zip for cromwell runs

    @kaijli
    kaijli committed Nov 14, 2023
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  3. Merge branch 'longreads' of https://github.com/microbiomedata/metaAss… 

    …embly into longreads
    @kaijli
    kaijli committed Nov 14, 2023
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  4. merged import lines

    @kaijli
    kaijli committed Nov 14, 2023
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  5. added test file

    @kaijli
    kaijli committed Nov 14, 2023
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  6. changed folder paths for nmdc edge server

    @kaijli
    kaijli committed Nov 14, 2023
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  7. Merge branch 'longreads' of https://github.com/microbiomedata/metaAss… 

    …embly into longreads
    @kaijli
    kaijli committed Nov 14, 2023
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  8. container issue in interleaved fixed

    @kaijli
    kaijli committed Nov 14, 2023
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  9. update jgi_meta_wdl submodules

    Chienchi Lo committed Nov 14, 2023
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  10. testing long reads

    @kaijli
    kaijli committed Nov 14, 2023
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Commits on Mar 8, 2024

  1. added makeinfo task. testing

    @kaijli
    kaijli committed Mar 8, 2024
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Commits on Apr 10, 2024

  1. added finishasm for long reads

    @kaijli
    kaijli committed Apr 10, 2024
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Commits on Apr 11, 2024

  1. small change to input_file name

    @kaijli
    kaijli committed Apr 11, 2024
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Commits on Apr 16, 2024

  1. added pipefail and symbolic link to all commands

    @kaijli
    kaijli committed Apr 16, 2024
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Commits on Apr 18, 2024

  1. changes for alicia

    @kaijli
    kaijli committed Apr 18, 2024
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  2. added set -euo pipefail to test_assembly

    @kaijli
    kaijli committed Apr 18, 2024
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  3. Merge pull request #17 from microbiomedata/longreads 

    Longreads update for assembly
    @kaijli
    kaijli authored Apr 18, 2024
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Commits on Apr 25, 2024

  1. Update version.txt 

    update version for long reads support
    @kaijli
    kaijli authored Apr 25, 2024
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  2. fixed typo in release creation

    @kaijli
    kaijli committed Apr 25, 2024
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  3. renamed files for release and consistency when running

    @kaijli
    kaijli committed Apr 25, 2024
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Commits on Apr 26, 2024

  1. Update create_release.yml 

    corrected typo for jgi_assembly.wdl
    @kaijli
    kaijli authored Apr 26, 2024
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  2. Update version.txt

    @kaijli
    kaijli authored Apr 26, 2024
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  3. Update version.txt

    @kaijli
    kaijli authored Apr 26, 2024
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  4. Update version.txt

    @kaijli
    kaijli authored Apr 26, 2024
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Commits on May 9, 2024

  1. Added potential fix for issue #18, needs testing

    Valerie Li committed May 9, 2024
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  2. forgot to ass short reads bbcms results to main assembly file

    @kaijli
    kaijli committed May 9, 2024
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Commits on Jun 4, 2024

  1. updated task finish_asm to accomodate issue #18

    @vlilanl
    vlilanl committed Jun 4, 2024
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Commits on Jun 11, 2024

  1. Changed a couple parameters to run on jaws and added hard and soft li… 

    …nks in shortReads_assembly.wdl
    @vlilanl
    vlilanl committed Jun 11, 2024
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  2. deleted sed command for bbcms.fastq.gz

    @vlilanl
    vlilanl committed Jun 11, 2024
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  3. Merge pull request #19 from microbiomedata/bbcmsouts 

    Shortreads bbcms #18
    @aclum
    aclum authored Jun 11, 2024
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  4. Update version.txt

    @vlilanl
    vlilanl authored Jun 11, 2024
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Commits on Oct 15, 2024

  1. removed unused git submodule, updated spades container

    @kaijli
    kaijli committed Oct 15, 2024
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  2. bump version

    @kaijli
    kaijli committed Oct 15, 2024
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  3. add runtime mem for interleave

    @kaijli
    kaijli committed Oct 15, 2024
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Commits on Oct 16, 2024

  1. remove extra comma

    @kaijli
    kaijli authored Oct 16, 2024
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Commits on Oct 20, 2024

  1. Merge pull request #24 from microbiomedata/23-update-to-spades-version-4 

    removed unused git submodule, updated spades container
    @kaijli
    kaijli authored Oct 20, 2024
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Commits on Nov 6, 2024

  1. fixed formatting and added in asmstats to metaflye.wdl

    @vlilanl
    vlilanl committed Nov 6, 2024
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Commits on Nov 7, 2024

  1. added stats.json as an output for task finish_lrasm

    @vlilanl
    vlilanl committed Nov 7, 2024
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  2. worflowmeta_contiainer -> workflowmeta_container

    @vlilanl
    vlilanl committed Nov 7, 2024
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  3. Updated bbtools container

    @vlilanl
    vlilanl committed Nov 7, 2024
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Commits on Nov 8, 2024

  1. reverted bbtools container for shortreads

    @vlilanl
    vlilanl committed Nov 8, 2024
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  2. Merge branch 'master' into 21-stats-file

    @vlilanl
    vlilanl authored Nov 8, 2024
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  3. formatting issues

    @vlilanl
    vlilanl committed Nov 8, 2024
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Commits on Nov 12, 2024

  1. Update index.rst

    @vlilanl
    vlilanl authored Nov 12, 2024
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  2. Updated image for documentation

    @vlilanl
    vlilanl committed Nov 12, 2024
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  3. Update version.txt

    @vlilanl
    vlilanl authored Nov 12, 2024
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  4. Update index.rst

    @vlilanl
    vlilanl authored Nov 12, 2024
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  5. Update index.rst

    @vlilanl
    vlilanl authored Nov 12, 2024
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  6. Update index.rst

    @vlilanl
    vlilanl authored Nov 12, 2024
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Commits on Nov 14, 2024

  1. Revert index.rst

    @vlilanl
    vlilanl authored Nov 14, 2024
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  2. Merge pull request #25 from microbiomedata/21-stats-file 

    21 Added in stats file for outputs
    @vlilanl
    vlilanl authored Nov 14, 2024
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Commits on Nov 15, 2024

  1. Update index.rst

    @vlilanl
    vlilanl authored Nov 15, 2024
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  2. Merge branch 'master' into documentation

    @vlilanl
    vlilanl authored Nov 15, 2024
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  3. Revert "Merge branch 'master' into documentation" 

    This reverts commit dbbfc10, reversing
changes made to b2cf317.

Formatting issues
    @vlilanl
    vlilanl committed Nov 15, 2024
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  4. Update index.rst

    @vlilanl
    vlilanl authored Nov 15, 2024
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  5. Update README.md

    @vlilanl
    vlilanl authored Nov 15, 2024
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  6. Update index.rst

    @vlilanl
    vlilanl authored Nov 15, 2024
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Commits on Nov 18, 2024

  1. Update bbtools container for short reads

    @vlilanl
    vlilanl committed Nov 18, 2024
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  2. Update version.txt

    @vlilanl
    vlilanl authored Nov 18, 2024
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  3. Update workflow diagram

    @vlilanl
    vlilanl committed Nov 18, 2024
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  4. Update version.txt

    @vlilanl
    vlilanl authored Nov 18, 2024
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  5. Merge pull request #26 from microbiomedata/documentation 

    Update Documentation and Update short reads bbtools container
    @vlilanl
    vlilanl authored Nov 18, 2024
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