Add gffread #29
Add gffread #29
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Hey @emmarousseau ! Thanks for creating this PR -- this already looks amazing!
I have some minor comments, see below :)
src/gffread/config.vsh.yaml
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| must_exist: false | ||
| description: | | ||
| Write the output records into <outfile> instead of stdout. |
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Make this a required argument -- the stdout produced by Viash components are only used for logging
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Can we give a default file name instead of making it required? So no output file needs to be specified and the usage syntax stays more similar to the original gffread
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If the component needs to return this file in order to function properly, please make it a required output file. This way, we can let Nextflow (and users) know which output files are expected and which are optional. I'll make a suggestion :)
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Thanks @emmarousseau! |
* Uploading local copy * Restructured directories and changed test data source and script * Create var/ssoftware_versions.txt * moved file and added quotes to all filenames * Small formatting changes, add command tag to config file * unset flags in script.sh and fixed argument types in config * Refined tests * Adjust comments * Add changelog description, add config keyword and reorder lines * Resolving the suggestions for PR 29 * Delete unused files * Make output file argument required
Description
Add gffread component.
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 gffreadCheck the correct box. Does this PR contain: