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33 Commits

Author SHA1 Message Date
CI
af7bcfffa4 Build branch main with version main (c733de2) 
Build pipeline: viash-hub.biobox.main-lltcw

Source commit: c733de2e4c

Source message: Bump viash to 0.9.4 (#175)

* Bump viash to 0.9.4

* Add CHANGELOG entry

* Add PR number
 2025-04-30 07:01:27 +00:00
CI
963503eca8 Build branch main with version main (1efc026) 
Build pipeline: viash-hub.biobox.main-kvvc8

Source commit: 1efc0264ca

Source message: Use `meta_name` instead of `meta_functionality_name` (#174)
 2025-04-22 09:13:11 +00:00
CI
a518d2ead8 Build branch main with version main (5f6516e) 
Build pipeline: viash-hub.biobox.main-v9whr

Source commit: 5f6516e9c0

Source message: Bump viash version (#172)

* bump viash version

* fix agat requirements
 2025-03-06 09:35:27 +00:00
CI
6f8d68b9cc Build branch main with version main (952ff08) 
Build pipeline: viash-hub.biobox.main-kwcc8

Source commit: 952ff08430

Source message: Update CHANGELOG for 0.3.0 release (#169)
 2024-12-03 10:54:51 +00:00
CI
38a478d5ae Build branch main with version main (a13b57d) 
Build pipeline: viash-hub.biobox.main-t7scl

Source commit: a13b57d04a

Source message: Add bases2fastq (#167)
 2024-11-26 14:40:26 +00:00
CI
6b56570131 Build branch main with version main (065297b) 
Build pipeline: viash-hub.biobox.main-nh6xw

Source commit: 065297be5f

Source message: Add sgdemux (#166)
 2024-11-14 13:36:35 +00:00
CI
dffc02813f Build branch main with version main (1d17ce0) 
Build pipeline: viash-hub.biobox.main-79vlw

Source commit: 1d17ce01e2

Source message: Add cellranger_mkref (#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
CI
b77e39f22a Build branch main with version main (b3fcd52) 
Build pipeline: viash-hub.biobox.main-8bbc7

Source commit: b3fcd52f20

Source message: Fix multiple components (#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
CI
c71aa10adc Build branch main with version main (06005a7) 
Build pipeline: viash-hub.biobox.main-s2mvx

Source commit: 06005a79b4

Source message: Add agat convert mfannot2gff (#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
CI
a7b0d33a32 Build branch main with version main (aa43543) 
Build pipeline: viash-hub.biobox.main-2k68h

Source commit: aa43543e1f

Source message: Rseqc innerdistance (#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
CI
35f315e911 Build branch main with version main (52f44f5) 
Build pipeline: viash-hub.biobox.main-xrs9m

Source commit: 52f44f5049

Source message: Add agat sp add introns (#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
CI
5ae0d0b0ba Build branch main with version main (6e6b139) 
Build pipeline: viash-hub.biobox.main-ndljn

Source commit: 6e6b13939c

Source message: nanoplot (#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
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
CI
db2f4203b8 Build branch main with version main (c3ba4a7) 
Build pipeline: viash-hub.biobox.main-n2mwd

Source commit: c3ba4a7849

Source message: Bcftools annotate (#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
CI
0075a8df93 Build branch main with version main (8fe9d66) 
Build pipeline: viash-hub.biobox.main-vhhxn

Source commit: 8fe9d66b0c

Source message: Bcftools stats (#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
CI
beb7940138 Build branch main with version main (320d044) 
Build pipeline: viash-hub.biobox.main-4vvfj

Source commit: 320d044fe4

Source message: Sortmerna (#146)
 2024-09-09 07:10:14 +00:00
CI
3f20a97c9c Build branch main with version main (9f81386) 
Build pipeline: viash-hub.biobox.main-tr92f

Source commit: 9f81386259

Source message: Fq subsample (#147)
 2024-09-09 06:40:11 +00:00
CI
ac86f27b69 Build branch main with version main (99dec59) 
Build pipeline: viash-hub.biobox.main-vzh9h

Source commit: 99dec5923b

Source message: Bedtools genomecov (#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
CI
ddad38b4a3 Build branch main with version main (e6627ec) 
Build pipeline: viash-hub.biobox.main-v4lxs

Source commit: e6627ec728

Source message: FastQC (#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
CI
f066ef0ffa Build branch main with version main (da3272d) 
Build pipeline: viash-hub.biobox.main-7x2wm

Source commit: da3272d011

Source message: Bcftools sort (#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