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cellranger_mkfastq_and_count.cwl
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cellranger_mkfastq_and_count.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "running cellranger mkfastq and count"
inputs:
bcl_directory:
type: Directory
chemistry:
type: string?
reference:
type: Directory
sample_name:
type: string
simple_sample_csv:
type: File
steps:
mkfastq:
run: ../tools/cellranger_mkfastq.cwl
in:
bcl_directory: bcl_directory
simple_sample_csv: simple_sample_csv
out: [samplesheet_csv, fastq_dir]
count:
run: ../tools/cellranger_count.cwl
in:
chemistry: chemistry
fastq_directory:
source: [mkfastq/fastq_dir]
linkMerge: merge_flattened
reference: reference
sample_name: sample_name
out: [out_dir]
outputs:
counts_out_dir:
type: Directory
outputSource: count/out_dir
fastqs:
type: Directory
outputSource: mkfastq/fastq_dir
samplesheet:
type: File
outputSource: mkfastq/samplesheet_csv