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change input type for finish_asm#9

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Michal-Babins wants to merge 102 commits intowerkflowmicrobiomedata/metaAssembly:werkflowfrom mastermicrobiomedata/metaAssembly:masterCopy head branch name to clipboard

+84,234-622

Commits

Commits on Dec 7, 2022

• change input type for finish_asm

  scanon

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  846ebf0

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Commits on Jan 28, 2023

• add make_info_file task

  

  Chienchi Lo

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• udpate README

  

  Chienchi Lo

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• fix missing make_info file direct

  

  Chienchi Lo

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Commits on Jun 10, 2023

• Merge pull request #11 from microbiomedata/make_info

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  scanon

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Commits on Jul 3, 2023

• added release workflow for assembly

  

  Michal-Babins

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• switched out uses for run

  

  Michal-Babins

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• removed v from version bump

  

  Michal-Babins

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Commits on Jul 6, 2023

• removed unused variables

  

  Michal-Babins

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Commits on Jul 10, 2023

• added version.txt and upated create_release.yml to source from version.txt

  

  Michal-Babins

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Commits on Jul 14, 2023

• remove unused input_file variable from finish_asm

  

  Michal-Babins

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Commits on Oct 17, 2023

• add jgi_meta_wdl submodules

  

  Chienchi Lo

  committed
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Commits on Oct 19, 2023

• changed wdl files to version 1.0

  kaijli

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Commits on Nov 3, 2023

• update jgi_meta_wdl submodules

  

  Chienchi Lo

  committed
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Commits on Nov 7, 2023

• quick script to choose between long and short reads

  kaijli

  committed
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Commits on Nov 9, 2023

• take one input either to long reads workflow or to short reads workflow

  

  Chienchi Lo

  committed
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Commits on Nov 12, 2023

• working on input dependencies

  kaijli

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• merged to include interleave

  kaijli

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• having trouble importing jgi long reads

  kaijli

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• quick json to test choice wdl

  kaijli

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Commits on Nov 13, 2023

• update jgi_meta_wdl submodules

  

  Chienchi Lo

  committed
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• move make_interleaved_reads into shortReads condition, and add container in interleaved_reads.wdl

  

  Chienchi Lo

  committed
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Commits on Nov 14, 2023

• working on file localization errors

  kaijli

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• added imports.zip for cromwell runs

  kaijli

  committed
  696579e

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• Merge branch 'longreads' of https://github.com/microbiomedata/metaAssembly into longreads

  kaijli

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• merged import lines

  kaijli

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• added test file

  kaijli

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• changed folder paths for nmdc edge server

  kaijli

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• Merge branch 'longreads' of https://github.com/microbiomedata/metaAssembly into longreads

  kaijli

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  1df1c4c

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• container issue in interleaved fixed

  kaijli

  committed
  7c7c4f8

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• update jgi_meta_wdl submodules

  

  Chienchi Lo

  committed
  789c936

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• testing long reads

  kaijli

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Commits on Mar 8, 2024

• added makeinfo task. testing

  kaijli

  committed
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Commits on Apr 10, 2024

• added finishasm for long reads

  kaijli

  committed
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Commits on Apr 11, 2024

• small change to input_file name

  kaijli

  committed
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Commits on Apr 16, 2024

• added pipefail and symbolic link to all commands

  kaijli

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Commits on Apr 18, 2024

• changes for alicia

  kaijli

  committed
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• added set -euo pipefail to test_assembly

  kaijli

  committed
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• Merge pull request #17 from microbiomedata/longreads

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  kaijli

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Commits on Apr 25, 2024

• Update version.txt

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  kaijli

  authored
  edfc408

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• fixed typo in release creation

  kaijli

  committed
  9901d31

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• renamed files for release and consistency when running

  kaijli

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Commits on Apr 26, 2024

• Update create_release.yml

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  kaijli

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• Update version.txt

  kaijli

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• Update version.txt

  kaijli

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• Update version.txt

  kaijli

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Commits on May 9, 2024

• Added potential fix for issue #18, needs testing

  

  Valerie Li

  committed
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• forgot to ass short reads bbcms results to main assembly file

  kaijli

  committed
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Commits on Jun 4, 2024

• updated task finish_asm to accomodate issue #18

  vlilanl

  committed
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Commits on Jun 11, 2024

• Changed a couple parameters to run on jaws and added hard and soft links in shortReads_assembly.wdl

  vlilanl

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• deleted sed command for bbcms.fastq.gz

  vlilanl

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• Merge pull request #19 from microbiomedata/bbcmsouts

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  aclum

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• Update version.txt

  vlilanl

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Commits on Oct 15, 2024

• removed unused git submodule, updated spades container

  kaijli

  committed
  8d0c90a

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• bump version

  kaijli

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  547f3a8

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• add runtime mem for interleave

  kaijli

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Commits on Oct 16, 2024

• remove extra comma

  kaijli

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Commits on Oct 20, 2024

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

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  kaijli

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Commits on Nov 6, 2024

• fixed formatting and added in asmstats to metaflye.wdl

  vlilanl

  committed
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Commits on Nov 7, 2024

• added stats.json as an output for task finish_lrasm

  vlilanl

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• worflowmeta_contiainer -> workflowmeta_container

  vlilanl

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• Updated bbtools container

  vlilanl

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Commits on Nov 8, 2024

• reverted bbtools container for shortreads

  vlilanl

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• Merge branch 'master' into 21-stats-file

  vlilanl

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• formatting issues

  vlilanl

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Commits on Nov 12, 2024

• Update index.rst

  vlilanl

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• Updated image for documentation

  vlilanl

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• Update version.txt

  vlilanl

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• Update index.rst

  vlilanl

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• Update index.rst

  vlilanl

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• Update index.rst

  vlilanl

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Commits on Nov 14, 2024

• Revert index.rst

  vlilanl

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• Merge pull request #25 from microbiomedata/21-stats-file

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  vlilanl

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Commits on Nov 15, 2024

• Update index.rst

  vlilanl

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• Merge branch 'master' into documentation

  vlilanl

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• Revert "Merge branch 'master' into documentation"

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  vlilanl

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• Update index.rst

  vlilanl

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• Update README.md

  vlilanl

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• Update index.rst

  vlilanl

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Commits on Nov 18, 2024

• Update bbtools container for short reads

  vlilanl

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• Update version.txt

  vlilanl

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• Update workflow diagram

  vlilanl

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• Update version.txt

  vlilanl

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• Merge pull request #26 from microbiomedata/documentation

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  vlilanl

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Commits on Nov 19, 2024

• Updated Workflow figure

  vlilanl

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• Merge pull request #27 from microbiomedata/documentation

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  vlilanl

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Commits on Dec 3, 2024

• update test data links

  kaijli

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Commits on Dec 5, 2024

• add svg

  kaijli

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• Update index.rst with svg

  kaijli

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• Merge pull request #29 from microbiomedata/28-generate-svg-version-of-diagram-and-update-indexrst-to-reference-it-instead-of-png-version

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  kaijli

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• remove image scale

  kaijli

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Commits on Dec 14, 2024

• Enable "Edit on GitHub" link by defining :github_url: in index.rst

  eecavanna

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• Merge pull request #31 from microbiomedata/30-configure-edit-on-github-link-by-adding-github_url-field-to-indexrst-file

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  eecavanna

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Commits on Feb 4, 2025

• Change String to File

  vlilanl

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• added in memory allocation for task stage

  vlilanl

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Commits on Feb 5, 2025

• changed String to File

  vlilanl

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Commits on Feb 22, 2025

• Update README.md

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  ssarrafan

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Commits on Feb 27, 2025

• Merge pull request #33 from microbiomedata/ssarrafan-patch-1

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  aclum

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Commits on Mar 3, 2025

• Update version.txt

  vlilanl

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• Merge pull request #32 from microbiomedata/tahoma

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  vlilanl

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Commits on Mar 5, 2025

• Update README.md

  kaijli

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• Update index.rst

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