FEAT: update busco to 5.7.1 #72
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dorien-er
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Jul 11, 2024
* FEAT: update busco to 5.7.1 * Typo
rcannood
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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]>
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Description
FEAT: update busco to 5.7.1
Issue ticket number
Closes #xxxxChecklist 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: