e3be4c4461
Build branch main with version main (b0db228)
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Build pipeline: viash-hub.biobox.main-nmzjs
Source commit: b0db228825#177 )
* update image
* add changelog
* make readme more generic
* fix url
* make images relative again
2025-05-06 20:36:16 +00:00
af7bcfffa4
Build branch main with version main (c733de2)
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Build pipeline: viash-hub.biobox.main-lltcw
Source commit: c733de2e4c#175 )
* Bump viash to 0.9.4
* Add CHANGELOG entry
* Add PR number
2025-04-30 07:01:27 +00:00
963503eca8
Build branch main with version main (1efc026)
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Build pipeline: viash-hub.biobox.main-kvvc8
Source commit: 1efc0264ca#174 )
2025-04-22 09:13:11 +00:00
a518d2ead8
Build branch main with version main (5f6516e)
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Build pipeline: viash-hub.biobox.main-v9whr
Source commit: 5f6516e9c0#172 )
* bump viash version
* fix agat requirements
2025-03-06 09:35:27 +00:00
6f8d68b9cc
Build branch main with version main (952ff08)
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Build pipeline: viash-hub.biobox.main-kwcc8
Source commit: 952ff08430#169 )
2024-12-03 10:54:51 +00:00
38a478d5ae
Build branch main with version main (a13b57d)
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Build pipeline: viash-hub.biobox.main-t7scl
Source commit: a13b57d04a#167 )
2024-11-26 14:40:26 +00:00
6b56570131
Build branch main with version main (065297b)
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Build pipeline: viash-hub.biobox.main-nh6xw
Source commit: 065297be5f#166 )
2024-11-14 13:36:35 +00:00
dffc02813f
Build branch main with version main (1d17ce0)
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Build pipeline: viash-hub.biobox.main-79vlw
Source commit: 1d17ce01e2#164 )
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* mkref component - config, test data, scripts, changelog
* Small updates
* Update CHANGELOG
* Update src/cellranger/cellranger_mkref/script.sh
---------
Co-authored-by: DriesSchaumont <5946712+DriesSchaumont@users.noreply.github.com >
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com >
2024-11-08 10:06:06 +00:00
b77e39f22a
Build branch main with version main (b3fcd52)
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Build pipeline: viash-hub.biobox.main-8bbc7
Source commit: b3fcd52f20#162 )
* output index when only_build_index is true
* fix threads option
* fix argument type and add log
* fix output handling
* fix output arguments and update docker image
* fix log2stderr argument and remove discard reads option
* remove echo
* update bbsplit build index test
* add workdir
* apply suggestions from code review
* accept more than two reference files
* update changelog
* update changelog
* remove indentation
* minor fixes
* fix descriptions
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com >
2024-11-08 09:40:57 +00:00
c71aa10adc
Build branch main with version main (06005a7)
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Build pipeline: viash-hub.biobox.main-s2mvx
Source commit: 06005a79b4#112 )
* add help
* add config
* add run script
* add test data and expected output + script to fetch them
* add test
* update changelog
* cleanup
* create temporary directory and clean up on exit
* add requirements
* update keywords
* update --config description
* add set -eo pipefail to script and test files
* fxi create temporary directory
* cleanup changelog
* cleanup changelog
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com >
2024-11-02 09:53:24 +00:00
a7b0d33a32
Build branch main with version main (aa43543)
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Build pipeline: viash-hub.biobox.main-2k68h
Source commit: aa43543e1f#159 )
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* full component with two tests
* fix default values
* adjust argument names and container image
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com >
2024-10-26 19:02:37 +00:00
35f315e911
Build branch main with version main (52f44f5)
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Build pipeline: viash-hub.biobox.main-xrs9m
Source commit: 52f44f5049#104 )
* add help
* add config
* add run script
* add test data and expected output + script to fetch them
* add tests
* update changelog
* Update src/agat/agat_sp_add_introns/config.vsh.yaml
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com >
* Update src/agat/agat_sp_add_introns/config.vsh.yaml
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com >
* Update src/agat/agat_sp_add_introns/config.vsh.yaml
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com >
* # create temporary directory and clean up on exit
* add set -e to test
* fix create temporary directory
* fix create temporary directory
* add set -eo pipefail to test
* add set -eo pipefail to script
* remove file added by mistake
* update --config description
* cleanup changelog
* cleanup changelog
* minor changes to config
* reduce test data size
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com >
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com >
Co-authored-by: Emma Rousseau <emmarou1@icloud.com >
2024-10-26 13:31:11 +00:00
5ae0d0b0ba
Build branch main with version main (6e6b139)
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Build pipeline: viash-hub.biobox.main-ndljn
Source commit: 6e6b13939c#95 )
* nanoplot
* test_data
* reinitiate
* gitignore
* namespace
* Testing NanoPlot in CLI
* NanoPlot complete
* Updated docker engine
* Docker
* Delete taget directory
* Deleted
* Input file
* fastq with more reads
* Delete config.vsh.yaml
* Pull request changes
* Delete var directory
* Config arguments complete
* Update help.txt
* Update config file
* Test files
* runners script
* gitignore default
* Move output
* Delete output directory
* Runners script complete
* Test script
* default output
* test data
* params passed correctly
* outdir
* test script
* input files
* all test files
* test data < 100 KB
* test script update
* Update CHANGELOG.md
* Update CHANGELOG.md
* Test cases in directories
* rm .gz .pickle .feather files
* reduce test input size
* Multiple separator ";" and check there is only one input file
---------
Co-authored-by: jakubmajercik <jakub.majercik@gmail.com >
Co-authored-by: Emma Rousseau <emmarou1@icloud.com >
2024-10-26 10:17:08 +00:00
0cdbd262c7
Build branch main with version main (7fb67a9)
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Build pipeline: viash-hub.biobox.main-zbkpz
Source commit: 7fb67a9853#138 )
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* initial commit, complete config file, add test data
* complete config file, adjusted script and tests, not functional
* update changelog, hep.txt, functional test, large test data
* smaller test data
* remove test resource from config
* modify paths in test script
* Arguments closer to original tool's
* Extra arg to allow use of bbmap args
2024-10-18 11:59:11 +00:00
