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
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>
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>
Build pipeline: viash-hub.biobox.main-lpdjj
Source commit: 766ab6c9c3
Source message: Qualimap rnaseq (#74)
* first version
* complete script for qualimap
* add escaping character before leading hashtag (#50)
* add escaping character before leading hashtag
* update changelog
* Update CHANGELOG.md
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* replace escaping \ by \\
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Samtools collate (#49)
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* Initial commit, whole component is functional
* Update viash (#51)
* update viash
* update readme
* update changelog
* update changelog
* fix incorrect heading detection
* update again
* clean up readme
* Samtools view (#48)
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* initial version with a few tests, script, and config file
* update changelog, add one test
* add a 4th test, fix option names in the script
* Fix name of component in config
* remove option named with a number
* add must_exist to input file argument
* removed "default: null" from one of the arguments in config
* remove utf8 characters from config
* Update CHANGELOG.md
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Samtools fastq (#52)
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* Initial commit, config, script, help and test_data
* Update changelog, add tests, fix argument naming errors, add test data
* update changelog, remove gffread namespace field
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* format URL in the description (#55)
* format URL in the description
* update changelog
* Change name in _viash.yaml (#60)
* Update operational code (#63)
* update readme
* switch ci to toolbox
* update to viash 0.9.0-RC6
* edit keywords
* fix version
* update biobox
* cutadapt (#7)
* First commit, clone of cutadapt in htrnaseq + help.txt
* Add config
* Don't allow multiple: true when providing a FASTA file with adapters
* First version of script
* Updates and fixes - se/pe
* Add tests and fix --json argument
* Add software version
* Better consistency in using snake_case
* Update src/cutadapt/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/cutadapt/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/cutadapt/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Specify --input and --input_r2 as separate arguments
* Avoid specifying default arg values
* Add more information to `--minimum_length` and `maximum_length`
* Add --cpus by means of $meta_cpus and set proper default
* Allow multiple for adapters/fasta and add test
* change multiple_sep to ';'
* add example
* simplify code with a helper function
* create directories in test
* use a different output extension if --fasta is provided
* decrease code duplication by separating optional outputs from paired/unpaired output arguments
* write custom tests for cutadapt
* fix _r2 arguments
* add debug flag as not to always print the cli command
* remove comment
* Update to Viash 0.9.0-RC4
* Ability to specify output globbing patterns
* Avoid the need for both output_dir and output
* Move fields from `info` to `links`
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Move references back to the info field
* apologies, I proposed a wrong syntax
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* update changelog
* update readme
* Update salmon quant arguments (#57)
* Make index an optional argument
* FIx argument type and add optional argument
* FEAT: add bedtools getfasta. (#59)
* FEAT: add bedtools getfasta.
* Add PR number to CHANGELOG
* Add star genomegenerate component (#58)
* Add star genomegenerate component
* Update changelog
* Rename component
* Update test
* Update CHANGELOG.md
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* fix package config (#65)
* Delete src/bgzip directory (#64)
It was moved to toolbox
* Output alignments to the transcriptome (#56)
* Output alignments to the transcriptome
* Change argument name
* BUG: pear component failure is ignored (#70)
* FEAT + BUG: cutadapt; allowing disabling demultiplexing and fix par_quality_cutoff_r2 (#69)
* FEAT: Disable cutadapt demultiplexing by default
* Cutadapt: fix --par_quality_cutoff_r2
* FEAT: update busco to 5.7.1 (#72)
* FEAT: update busco to 5.7.1
* Typo
* Samtools fasta (#53)
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* Fasta component
* change script resource to samtools_fastq script, with dummy argument to specify the command
* add dummy argument to samtools_fastq to share the script with samtools_fasta
* fix path to script in config
* Update src/samtools/samtools_fastq/script.sh
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Change default fields to examples
* Two more default fields changed to examples
* Minor formatting changes
* Markdown formatting changes in configs
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Umi tools dedup (#54)
* initial commit dedup
* Revert "initial commit dedup"
This reverts commit 38f586bec0ac9e4312b016e29c3aa0bd53f292b2.
* inital commit dedup
* Working component with one test
* Update test 1 and test data, fix some arg types in config and script
* test data files and changes to script
* Add third test and test data
* Fix typo in script
* remove utf8 characters in config
* Add choices fields and change default fields to exampels
* Minor formatting changes
* md formatting changes in config
* Fix typo (#79)
* add vscode to gitignore
* update multiple separator (#81)
* update multiple separator
* update changelog
* Update src/multiqc/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/multiqc/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/multiqc/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/multiqc/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* update ifs
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* add test data
* add tests
* update changelog
* remove unrequired test data
* update descriptions
* update changelog
* update help text
* Update src/qualimap/qualimap_rnaseq/script.sh
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* update unit tests
* update unit tests
* addres pr changes request
* add version
* remove whitespace multiqc
* Apply suggestions from code review
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* address pr comments
* Update CHANGELOG.md
* fix doi
* Fix name
* update version and container image
* write software version to file
---------
Co-authored-by: dorien-er <roosen.dorien@gmail.com>
Co-authored-by: Leila011 <leilapaquay@gmail.com>
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Co-authored-by: emmarousseau <emmarou1@icloud.com>
Co-authored-by: Sai Nirmayi Yasa <92786623+sainirmayi@users.noreply.github.com>
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Co-authored-by: Dorien <41797896+dorien-er@users.noreply.github.com>
Build pipeline: viash-hub.biobox.main-rgg5q
Source commit: 4aa0a893d2
Source message: Add agat convert bed2gff (#97)
* add config
* add help
* add script
* add test data and expected output file
* add script to get test data
* add tests
* update changelog
* fix path to test data
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
Build pipeline: viash-hub.biobox.main-7dwhr
Source commit: da414e72c6
Source message: Add star solo component (#62)
* add star solo component
* change arguments from camelCase to snake_case
* get rid of multiple_sep
* drop star_solo component and just add arguments to star_align_reads
* Update src/star/star_align_reads/script.py
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
---------
Co-authored-by: Dries Schaumont <5946712+DriesSchaumont@users.noreply.github.com>
Build pipeline: viash-hub.biobox.main-2mtst
Source commit: 3481750f6e
Source message: Output alignments to the transcriptome (#56)
* Output alignments to the transcriptome
* Change argument name
