/
salmon-quantification.cwl
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salmon-quantification.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
cwlVersion: v1.0
label: Salmon quantification, FASTQ -> H5AD count matrix
inputs:
fastq_dir:
label: "Directory containing FASTQ files"
type: Directory[]
assay:
label: "scRNA-seq assay"
type: string
threads:
label: "Number of threads for Salmon"
type: int
default: 1
expected_cell_count:
type: int?
keep_all_barcodes:
type: boolean?
outputs:
salmon_output:
outputSource: salmon/output_dir
type: Directory
label: "Full output of `salmon alevin`"
count_matrix_h5ad:
outputSource: annotate_cells/annotated_h5ad_file
type: File
label: "Unfiltered count matrix from Alevin, converted to H5AD, spliced and unspliced counts"
raw_count_matrix:
outputSource: alevin_to_anndata/raw_expr_h5ad
type: File
label: "Unfiltered count matrix from Alevin, converted to H5AD, with intronic counts as separate columns"
genome_build_json:
outputSource: alevin_to_anndata/genome_build_json
type: File
label: "Genome build information in JSON format"
steps:
adjust_barcodes:
in:
fastq_dir:
source: fastq_dir
assay:
source: assay
out: [adj_fastq_dir, metadata_json]
run: salmon-quantification/adjust-barcodes.cwl
trim_reads:
in:
orig_fastq_dirs:
source: fastq_dir
adj_fastq_dir:
source: adjust_barcodes/adj_fastq_dir
assay:
source: assay
threads:
source: threads
out: [trimmed_fastq_dir]
run: salmon-quantification/trim-reads.cwl
salmon:
in:
orig_fastq_dirs:
source: fastq_dir
trimmed_fastq_dir:
source: trim_reads/trimmed_fastq_dir
assay:
source: assay
threads:
source: threads
expected_cell_count:
source: expected_cell_count
keep_all_barcodes:
source: keep_all_barcodes
out:
- output_dir
run: salmon-quantification/salmon.cwl
label: "Salmon Alevin, with index from GRCh38 transcriptome"
alevin_to_anndata:
in:
alevin_dir:
source: salmon/output_dir
out:
- expr_h5ad
- raw_expr_h5ad
- genome_build_json
run: salmon-quantification/alevin-to-anndata.cwl
label: "Convert Alevin output to AnnData object in h5ad format"
annotate_cells:
in:
orig_fastq_dirs:
source: fastq_dir
assay:
source: assay
h5ad_file:
source: alevin_to_anndata/expr_h5ad
metadata_json:
source: adjust_barcodes/metadata_json
out:
- annotated_h5ad_file
run: salmon-quantification/annotate-cells.cwl