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icgc-argo / workflow-roadmap

Roadmap and management for genomic data processing
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Update Stage_input subworkflow to accommodate RNAseq data #440

Closed guanqiaofeng closed 4 months ago

guanqiaofeng commented 5 months ago

Current Stage_input subworkflow could process RNAseq data by study_id and analysis_id input, could not process by samplesheet input. This need to be updated.

For RNAseq data, library_strandedness is required for Hisat2 aligner. However library_strandedness is not captured in metadata in current Stage_input subworkflow. Need to update the meta data to include library_strandedness.

Check to confirm whether sequencing_date need to be included in metadata.

guanqiaofeng commented 5 months ago

https://github.com/icgc-argo-workflows/argo-modules/pull/38

guanqiaofeng commented 4 months ago

closing as completed