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cellranger_count_0.0.3.wdl
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cellranger_count_0.0.3.wdl
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version 1.0
workflow cellranger_count_workflow {
input {
String fastq_file_paths
String reference_genome
String run_id
}
call run_cellranger_count {
input:
fastq_file_paths = fastq_file_paths,
reference_genome = reference_genome,
run_id = run_id
}
}
task run_cellranger_count {
input {
String fastq_file_paths
String reference_genome
String run_id
}
command {
cellranger count \
--id ~{run_id} \
--fastqs ~{fastq_file_paths} \
--transcriptome ~{reference_genome} \
--localcores=8 \
--localmem=32
}
output {
File output_count_directory = "~{run_id}/outs"
File output_metrics_summary = "~{run_id}/outs/metrics_summary.csv"
File output_web_summary = "~{run_id}/outs/web_summary.html"
}
runtime {
docker: "nfcore/cellranger:7.2.0"
cpu: "8"
memory: "32 GB"
disk: "local-disk 300 HDD"
}
}