fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex
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Tests This workflow processes the CMO fastqs with CITE-seq-Count and include the translation step required for cellPlex processing. In parallel it processes the Gene Expresion fastqs with STARsolo, filter cells with DropletUtils and reformat all outputs to be easily used by the function 'Read10X' from Seurat.
Steps
| ID | Name | Description |
|---|---|---|
| 8 | process GEX reads | n/a |
| 9 | CITE-seq-Count | toolshed.g2.bx.psu.edu/repos/iuc/cite_seq_count/cite_seq_count/1.4.4+galaxy0 |
| 10 | Rename STAR-solo output | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
| 11 | translate 10x barcode v2 to 10x barcode v1 | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2 |
| 12 | Re-organize CITE-seq-Count output | n/a |
| 13 | rename CITE-seq output | toolshed.g2.bx.psu.edu/repos/iuc/pick_value/pick_value/0.2.0 |
Version History
v0.6.5 (latest) Created 8th Apr 2026 at 03:01 by WorkflowHub Bot
Updated to v0.6.5
Frozen
v0.6.5cc2192f
v0.1 (earliest) Created 22nd Dec 2023 at 03:01 by WorkflowHub Bot
Updated to v0.1
Frozen
v0.1
bdf1e0d
Creators and SubmitterViews: 10493 Downloads: 33765 Runs: 0
Created: 22nd Dec 2023 at 03:01
Last updated: 20th Aug 2025 at 10:29
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