Add salmon #24
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Add salmon #24
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I merged the PR that upgrades the viash version in biobase to 0.9. Could you update this PR to the Viash 0.9 format? 🙇 Thanks! |
rcannood
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Feb 27, 2024
src/salmon/quant/test_data/salmon/transcriptome_index/complete_ref_lens.bin
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rcannood
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Mar 21, 2024
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rcannood
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Mar 25, 2024
emmarousseau
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Mar 29, 2024
commit d9e7fdf Author: Sai Nirmayi Yasa <[email protected]> Date: Thu Mar 28 20:08:30 2024 +0530 Add salmon (viash-hub#24) * add salmon index and quant * add test resources * add help text * script and config * add test * update script and test * add salmon quant * update CHANGELOG.md * update to viash 0.9 format * remove echo ststement * output the main salmon output file separately * check if output file has the right columns * check if correct output files were generated * fix doi Co-authored-by: Robrecht Cannoodt <[email protected]> * use the default multiple separator * rename components * remove print statements * check info.json output * reduce size of fastq files and generate index in test script * use smaller (manual) test data * set A as the default lib_type * Merge branch 'add_salmon' of https://github.com/viash-hub/biobase into add_salmon * add test to check content of output index * add more detailed description about libType * add test data * delete test data * move to salmon_index and salmon_quant --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
emmarousseau
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Mar 29, 2024
* add salmon index and quant * add test resources * add help text * script and config * add test * update script and test * add salmon quant * update CHANGELOG.md * update to viash 0.9 format * remove echo ststement * output the main salmon output file separately * check if output file has the right columns * check if correct output files were generated * fix doi Co-authored-by: Robrecht Cannoodt <[email protected]> * use the default multiple separator * rename components * remove print statements * check info.json output * reduce size of fastq files and generate index in test script * use smaller (manual) test data * set A as the default lib_type * Merge branch 'add_salmon' of https://github.com/viash-hub/biobase into add_salmon * add test to check content of output index * add more detailed description about libType * add test data * delete test data * move to salmon_index and salmon_quant --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
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Description
Add salmon index and quant components
Issue ticket number
Closes #xxxx
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: