09f5294af0
Build branch main with version main (add1252)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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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)
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Build pipeline: viash-hub.biobox.main-69lmq
Source commit: 80aaf333dc#149 )
2024-09-13 07:30:50 +00:00
cccb2f63f6
Build branch main with version main (bd8ca88)
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Build pipeline: viash-hub.biobox.main-t28sb
Source commit: bd8ca889d1#145 )
* Initial Commint
* Create help.txt
* Update config.vsh.yaml
* Update config.vsh.yaml
* Update config.vsh.yaml
* Update script.sh
* add template for tests
* Update test.sh
* small changes in config file
* adding more tests
* adding more test
* Update CHANGELOG.md
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com >
2024-09-10 14:36:19 +00:00
2a330fe450
Build branch main with version main (dc7b33d)
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Build pipeline: viash-hub.biobox.main-62lvg
Source commit: dc7b33d51f#144 )
* Initial Commit
* config and help.txt
* script.sh
* test template
* More tests and debugging
* test 5 and 6
* test 7, 8, 9
* Update test.sh
* fixing bug on config
* Changelog
* Update config.vsh.yaml
* Requested changes
* Bug fixing
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com >
2024-09-10 14:36:08 +00:00
db2f4203b8
Build branch main with version main (c3ba4a7)
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Build pipeline: viash-hub.biobox.main-n2mwd
Source commit: c3ba4a7849#143 )
* Initial commit
* Update config.vsh.yaml
* changes in config file
* Update script.sh
* Help File
* Update script.sh
* Update test.sh
* bug fixing and adding tests
* Update test.sh
* Update test.sh
* adding 3rd test
* More tests
* Moreee tests
* Update test.sh
* small changes
* Update CHANGELOG.md
* Update config.vsh.yaml
* bug fixing on config
* Requested changes
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com >
2024-09-10 14:11:21 +00:00
0075a8df93
Build branch main with version main (8fe9d66)
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Build pipeline: viash-hub.biobox.main-vhhxn
Source commit: 8fe9d66b0c#142 )
* Initial Commit
* Adding options to config
* Update on script
* update
* Adding test 2 and 3
* Update on config and test
* adding more tests
* debugging and adding tests
* Adding last tests
* removing test_data dir
* Update CHANGELOG.md
* small changes
* small change in help file
* Requested changes
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com >
2024-09-10 14:10:14 +00:00
beb7940138
Build branch main with version main (320d044)
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Build pipeline: viash-hub.biobox.main-4vvfj
Source commit: 320d044fe4#146 )
2024-09-09 07:10:14 +00:00
3f20a97c9c
Build branch main with version main (9f81386)
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Build pipeline: viash-hub.biobox.main-tr92f
Source commit: 9f81386259#147 )
2024-09-09 06:40:11 +00:00
ac86f27b69
Build branch main with version main (99dec59)
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Build pipeline: viash-hub.biobox.main-vzh9h
Source commit: 99dec5923b#150 and #128 )
* Initial commit
* Update config.vsh.yaml
* Update script.sh
* update on test.sh
* bug fixing
* adding ibam option tests
* depthzero and strand option tests
* 5prime and max tests
* more tests
* Changelog
* Update config.vsh.yaml
* Update config.vsh.yaml
* Update script.sh
* Update test.sh
* TMPDIR
* Unset Variables
* par_trackopts multiple: true
* Minor update to CHANGELOG
---------
Co-authored-by: tgaspe <theodorogtc@gmail.com >
2024-09-06 22:05:55 +00:00
ddad38b4a3
Build branch main with version main (e6627ec)
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Build pipeline: viash-hub.biobox.main-v4lxs
Source commit: e6627ec728#92 )
* Starting Component
* Creating Files
* update on config file
* Update on test.sh
* Update on config
* Update script.sh
* Update on script.sh
* trying to figure multiple: true
* Update on script.sh
* Update on script
* Adding some tests
* More tests
* Update on script.sh
* Added more tests
* Small Changes
* Update test.sh
* Update on Script and Test
- change the --zip and --html to take wild card '*'
* Added one more test
* Removed test_data dir
* More description
* Update CHANGELOG.md
* Update on config and script
- meta_cpus
- meta_tmp_dir
* Bug Fixed
* unset_if_false
* Updating Tests
* Update script.sh
* debugging
* Minor changes
* Update config.vsh.yaml
* Update config.vsh.yaml
* Required Changes
- large changes on script.sh
* Update config.vsh.yaml
* Adding extra links
* tmpdir bug
* Updating tests
* minor changes
* Adding extra output options
--summary
--data
* minor change
* Update script.sh
* small change in config
2024-09-03 09:13:58 +00:00
f066ef0ffa
Build branch main with version main (da3272d)
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Build pipeline: viash-hub.biobox.main-7x2wm
Source commit: da3272d011#141 )
* Initial commit
* Update on config file
* Update
* Update config.vsh.yaml
* Update config.vsh.yaml
* Update test.sh
* Update help.txt
* adding meta variables
* Adding test for bcf file
* Update CHANGELOG.md
* Update config.vsh.yaml
* requested changes
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com >
2024-09-02 13:42:09 +00:00
7dd88311d4
Build branch main with version main (f3e87e5)
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Build pipeline: viash-hub.biobox.main-7qmtp
Source commit: f3e87e58c9#140 )
* Initial commit
* Update test.sh
* help file + n option
* adding n_score option
* small changes
* Update CHANGELOG.md
* Update CHANGELOG.md
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com >
2024-09-02 13:25:01 +00:00
18d6cad4c4
Build branch main with version main (2b29a47)
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Build pipeline: viash-hub.biobox.main-bjgnf
Source commit: 2b29a47575#123 )
* Initial Commit
* Update config.vsh.yaml
* config file
* script.sh
* adding some tests
* more test
* Update CHANGELOG.md
* deleted test_data
* bug fix
* Update config.vsh.yaml
* adding more links
* exit on error
* $TMPDIR
* Update script.sh
* Update config.vsh.yaml
* Suggested change on column option
---------
Co-authored-by: Jakub Majercik <57993790+jakubmajercik@users.noreply.github.com >
2024-09-02 13:18:11 +00:00
