vsh/biobox
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity
33 Commits 23 Branches 7 Tags
0cdbd262c713e95f99efa4920403a1f622c41c40
Commit Graph

14 Commits

Author SHA1 Message Date
CI
0cdbd262c7 Build branch main with version main (7fb67a9) 
Build pipeline: viash-hub.biobox.main-zbkpz

Source commit: 7fb67a9853

Source message: Add bbmap_bbsplit (#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
CI
55de3a494d Build branch main with version main (86333c1) 
Build pipeline: meta-vsh-ci-template-tpwsr

Source commit: 86333c1a46

Source message: SnpEff (#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
CI
09f5294af0 Build branch main with version main (add1252) 
Build pipeline: viash-hub.biobox.main-bv4sf

Source commit: add125261c

Source message: FEAT: avoid using boolean_false (#160)
 2024-10-07 09:26:30 +00:00
CI
adf9159264 Build branch main with version main (0a0edca) 
Build pipeline: viash-hub.biobox.main-77vkl

Source commit: 0a0edcacb5

Source message: Cutadapt: fix non-functional action parameter (#161)

* Cutadapt: fix non-functional action parameter

* Add PR number
 2024-10-03 13:08:17 +00:00
CI
99b76ba2a1 Build branch main with version main (237a2e3) 
Build pipeline: viash-hub.biobox.main-dqhhg

Source commit: 237a2e3a22

Source message: Fixes the typo raised in issue #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
CI
6a8cd85cf3 Build branch main with version main (bc9cc0a) 
Build pipeline: viash-hub.biobox.main-bd96b

Source commit: bc9cc0a6ce

Source message: Kallisto quant (#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
CI
bca90c9331 Build branch main with version main (619f1bb) 
Build pipeline: viash-hub.biobox.main-wqbh6

Source commit: 619f1bbb6d

Source message: Rsem-calculate-expression (#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
CI
6f2f840fd9 Build branch main with version main (7f8bcc2) 
Build pipeline: viash-hub.biobox.main-zp6tq

Source commit: 7f8bcc2b3e

Source message: BD rhapsody sequence analysis (#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
CI
f47054953e Build branch main with version main (38f635a) 
Build pipeline: viash-hub.biobox.main-dz9k8

Source commit: 38f635ad57

Source message: Add agat convert genscan2gff (#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
CI
4b61e09a56 Build branch main with version main (124d50c) 
Build pipeline: viash-hub.biobox.main-pjlfn

Source commit: 124d50ce53

Source message: update changelog for viash 0.2.0
 2024-09-16 08:16:27 +00:00
CI
97f1502b57 Build branch main with version main (fe56ee7) 
Build pipeline: viash-hub.biobox.main-fjg6k

Source commit: fe56ee7c53

Source message: change output quant file to an optional argument (#151)
 2024-09-13 07:33:08 +00:00
CI
af89cea364 Build branch main with version main (80aaf33) 
Build pipeline: viash-hub.biobox.main-69lmq

Source commit: 80aaf333dc

Source message: Add Kallisto index (#149)
 2024-09-13 07:30:50 +00:00
CI
cccb2f63f6 Build branch main with version main (bd8ca88) 
Build pipeline: viash-hub.biobox.main-t28sb

Source commit: bd8ca889d1

Source message: Bcftools Concat (#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
CI
2a330fe450 Build branch main with version main (dc7b33d) 
Build pipeline: viash-hub.biobox.main-62lvg

Source commit: dc7b33d51f

Source message: Bcftools Norm (#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