Lk add starsolo barcode metrics #1044
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…broadinstitute/warp into lk-add-starsolo-barcode-metrics
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tasks/skylab/StarAlign.wdl
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| File align_features_sn_rna = "Features_sn_rna.stats" | ||
| File summary_sn_rna = "Summary_sn_rna.csv" | ||
| File umipercell_sn_rna = "UMIperCellSorted_sn_rna.txt" | ||
| #File aligner_metrics = "~{output_bam_basename}.star_metrics.tar" |
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do we still want this commented out?
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Thanks for catching it. I'm going to delete it entirely.
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| @@ -337,31 +338,52 @@ task STARsoloFastq { | |||
| --soloUMIdedup 1MM_Directional_UMItools \ | |||
| --outSAMtype BAM SortedByCoordinate \ | |||
| --outSAMattributes UB UR UY CR CB CY NH GX GN \ | |||
| --soloBarcodeReadLength 0 | |||
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Do we typically run star twice? Is it possible to run it just once?
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We run it twice for the count_exons = true. With the latest version of STAR, we should be able to run both parameters in a single STAR run. We haven't yet played with that functionality.
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retest this please |
Description
We've had requests to include STARsolo per barcode metrics as an output to the Optimus workflow. This PR creates a new output (aligner_metrics) that includes the combined per barcode metrics across all shards to the Starsolo alignment task.
Checklist
If you can answer "yes" to the following items, please add a checkmark next to the appropriate checklist item(s) and notify our WARP documentation team by tagging either @ekiernan or @kayleemathews in a comment on this PR.