Add tximport module (port from rnaseq) #4884
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pinin4fjords
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maxulysse
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Feb 8, 2024
maxulysse
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Feb 8, 2024
Co-authored-by: Maxime U Garcia <[email protected]>
adamrtalbot
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Feb 8, 2024
| read_transcript_info <- function(tinfo_path){ | ||
| info <- file.info(tinfo_path) | ||
| if (info\$size == 0) { | ||
| stop("tx2gene file is empty") |
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Today I learnt about stop in R!
| @@ -0,0 +1,227 @@ | |||
| #!/usr/bin/env Rscript | |||
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Does this need --vanilla?
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Possibly. I'm mucking about with the three related r modules right now, I'll add it in another PR
This was referenced Feb 12, 2024
jch-13
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Mar 19, 2024
* Add tximport module * Populate meta * Fix up tximport * Appease eclint * Fix conda * Fix singularity * Update test_data.config * poke ci * remove rogue empty line * Update tests/config/test_data.config Co-authored-by: Maxime U Garcia <[email protected]> --------- Co-authored-by: Maxime U Garcia <[email protected]>
jennylsmith
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Mar 20, 2024
* Add tximport module * Populate meta * Fix up tximport * Appease eclint * Fix conda * Fix singularity * Update test_data.config * poke ci * remove rogue empty line * Update tests/config/test_data.config Co-authored-by: Maxime U Garcia <[email protected]> --------- Co-authored-by: Maxime U Garcia <[email protected]>
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nf-core/test-datasets#1088 needs to be merged first, and test data link corrected here.PR checklist
versions.ymlfile.labelPROFILE=docker pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=singularity pytest --tag <MODULE> --symlink --keep-workflow-wd --git-awarePROFILE=conda pytest --tag <MODULE> --symlink --keep-workflow-wd --git-aware