Workflow: Salmon quantification, FASTQ -> H5AD count matrix

Fetched 2024-11-09 20:50:33 GMT
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Inputs

ID Type Title Doc
assay String scRNA-seq assay
img_dir Directory (Optional)
threads Integer Number of threads for Salmon
organism String (Optional)
fastq_dir Directory[] Directory containing FASTQ files
metadata_dir Directory (Optional)
keep_all_barcodes Boolean (Optional)
expected_cell_count Integer (Optional)

Steps

ID Runs Label Doc
salmon
salmon-quantification/salmon.cwl (CommandLineTool)
Run Salmon Alevin tool on FASTQ input
trim_reads
salmon-quantification/trim-reads.cwl (CommandLineTool)
Trim FASTQ files
salmon-mouse
salmon-quantification/salmon-mouse.cwl (CommandLineTool)
Run Salmon Alevin tool on FASTQ input
annotate_cells
salmon-quantification/annotate-cells.cwl (CommandLineTool)
Assay-specific annotation of cell barcodes after quantification
adjust_barcodes
salmon-quantification/adjust-barcodes.cwl (CommandLineTool)
Assay-specific adjustment of cell barcodes
alevin_to_anndata
salmon-quantification/alevin-to-anndata.cwl (CommandLineTool)
Convert Alevin sparse output to anndata.AnnData object, save as h5ad

Outputs

ID Type Label Doc
salmon_output Directory Full output of `salmon alevin`
raw_count_matrix File (Optional) Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts as separate columns
count_matrix_h5ad File Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts
genome_build_json File Genome build information in JSON format
Permalink: https://w3id.org/cwl/view/git/69da10ae891ce1ea821a59b9d0f33c9b931c88a9/steps/salmon-quantification.cwl