a7b0d33a32
Build branch main with version main (aa43543)
...
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)
...
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)
...
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)
...
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
55de3a494d
Build branch main with version main (86333c1)
...
Build pipeline: meta-vsh-ci-template-tpwsr
Source commit: 86333c1a46#153 )
* Help file
* config file
* config file
* runners script
* config file
* test script
* test
* test
* runners script
* snake case
* snake case
* output parameters
* modify argument formatting, container setup
* fix buf with mv command
* avoid boolean_false and fix bug with output files
---------
Co-authored-by: Emma Rousseau <emmarou1@icloud.com >
2024-10-16 09:18:30 +00:00
09f5294af0
Build branch main with version main (add1252)
...
Build pipeline: viash-hub.biobox.main-bv4sf
Source commit: add125261c#160 )
2024-10-07 09:26:30 +00:00
adf9159264
Build branch main with version main (0a0edca)
...
Build pipeline: viash-hub.biobox.main-77vkl
Source commit: 0a0edcacb5#161 )
* Cutadapt: fix non-functional action parameter
* Add PR number
2024-10-03 13:08:17 +00:00
99b76ba2a1
Build branch main with version main (237a2e3)
...
Build pipeline: viash-hub.biobox.main-dqhhg
Source commit: 237a2e3a22#132 (#157 )
* Fixes the typo raised in issue #132
* Add changelog entry
* fix typo, modify script
---------
Co-authored-by: jakubmajercik <jakub.majercik@gmail.com >
2024-09-27 10:17:59 +00:00
6a8cd85cf3
Build branch main with version main (bc9cc0a)
...
Build pipeline: viash-hub.biobox.main-bd96b
Source commit: bc9cc0a6ce#152 )
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* complete component
* Update changelog
* add help.txt
* apply suggested changes (changelog, config)
2024-09-19 04:13:10 +00:00
bca90c9331
Build branch main with version main (619f1bb)
...
Build pipeline: viash-hub.biobox.main-wqbh6
Source commit: 619f1bbb6d#93 )
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* three rsem components initial commit
* update container setup
* Simplified container configuration
* temporarily remove version recording from config
* Complete config file
* add tests and complete config file
* change test dataset
* functional test, adjustements to scripts
* Update changelog
* Simplified test data and help.txt contents
* suggested changes, typos
* simplify, get rid of test_data folder
* Update CHANGELOG.md
* Update CHANGELOG.md
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com >
2024-09-18 14:13:01 +00:00
6f2f840fd9
Build branch main with version main (7f8bcc2)
...
Build pipeline: viash-hub.biobox.main-zp6tq
Source commit: 7f8bcc2b3e#96 )
* wip
* fix test
* add help
* update 2.2 args
* fix bug
* extend test data
* output separate files
* analyse missing args
* tweaks to test
* fix script
* fix test
* fix test
* move small reference
* wip generate wta test data
* don't forget about umi in r1
* remove unneeded pkg
* load reference in memory just once
* fix random choices
* extend test
* add abc immunediscoverypanel
* wip abc testing code
* fix abc test; need unique instrument, run and flowcell ids for each sample
* add smk data
* add entry to changelog
* remove old test file
* adapt test for missing read
* update description
* add comment
* ensure cwl files are absolute
* Apply suggestions from code review
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com >
* fix suggestion
* newer pipelines have docker requirements as a hint instead of a strict requirement
* rename str to content
* remove deleted resources
* fix containers
* fix script
* fix suggestion
* fix suggestion...
* fix test
* fix component name
* fix test
* apply suggestions
* fix test
* added note
* fix changelog
* fix changelog again
* splitting hairs here
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com >
2024-09-17 10:13:18 +00:00
f47054953e
Build branch main with version main (38f635a)
...
Build pipeline: viash-hub.biobox.main-dz9k8
Source commit: 38f635ad57#100 )
* add config
* add help
* add test data and expected output adn the script to obtain them
* add running script
* add test script
* update changelog
* cleanup
* fix tests
* format description
* remove unused argument --inflate-off
* update --config description
* add requirements
* create temporary directory and clean up on exit
* add GENSCAN in keywords
* add set -e to test
* fix create temporary directory
* add set -eo pipefail to test
* add set -eo pipefail to script
* fix create temporary directory
* update --config description
* cleanup changelog
* cleanup changelog
* Update deprecated variable
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com >
2024-09-17 07:19:20 +00:00
4b61e09a56
Build branch main with version main (124d50c)
...
Build pipeline: viash-hub.biobox.main-pjlfn
Source commit: 124d50ce53
2024-09-16 08:16:27 +00:00
97f1502b57
Build branch main with version main (fe56ee7)
...
Build pipeline: viash-hub.biobox.main-fjg6k
Source commit: fe56ee7c53#151 )
2024-09-13 07:33:08 +00:00
af89cea364
Build branch main with version main (80aaf33)
...
Build pipeline: viash-hub.biobox.main-69lmq
Source commit: 80aaf333dc#149 )
2024-09-13 07:30:50 +00:00
