update multiple separator #81
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
rcannood
requested changes
Jul 11, 2024
Co-authored-by: Robrecht Cannoodt <[email protected]>
Co-authored-by: Robrecht Cannoodt <[email protected]>
Co-authored-by: Robrecht Cannoodt <[email protected]>
Co-authored-by: Robrecht Cannoodt <[email protected]>
rcannood
approved these changes
Jul 11, 2024
dorien-er
added a commit
that referenced
this pull request
Jul 11, 2024
* update multiple separator * update changelog * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * update ifs --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
rcannood
added a commit
that referenced
this pull request
Aug 21, 2024
* 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 <[email protected]> * replace escaping \ by \\ --------- Co-authored-by: Robrecht Cannoodt <[email protected]> * Samtools collate (#49) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586b. * 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 38f586b. * 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 <[email protected]> * Samtools fastq (#52) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586b. * 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 <[email protected]> * 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 <[email protected]> * Update src/cutadapt/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/cutadapt/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * 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 <[email protected]> * Move references back to the info field * apologies, I proposed a wrong syntax --------- Co-authored-by: Robrecht Cannoodt <[email protected]> * 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 <[email protected]> * 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 38f586b. * 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 <[email protected]> * 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 <[email protected]> * Umi tools dedup (#54) * initial commit dedup * Revert "initial commit dedup" This reverts commit 38f586b. * 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 <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * Update src/multiqc/config.vsh.yaml Co-authored-by: Robrecht Cannoodt <[email protected]> * update ifs --------- Co-authored-by: Robrecht Cannoodt <[email protected]> * 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 <[email protected]> * 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 <[email protected]> * 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 <[email protected]> Co-authored-by: Leila011 <[email protected]> Co-authored-by: Robrecht Cannoodt <[email protected]> Co-authored-by: emmarousseau <[email protected]> Co-authored-by: Sai Nirmayi Yasa <[email protected]> Co-authored-by: Dries Schaumont <[email protected]> Co-authored-by: Dorien <[email protected]>
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Description
update multiple separator to default
;Issue ticket number
(Partially) closes #77
Checklist before requesting a review
I have performed a self-review of my code
Conforms to the Contributing guidelines
Proposed changes are described in the CHANGELOG.md
I have tested my code with
viash ns test --parallel -q <name or namespace>Check the correct box. Does this PR contain: