biomodalQC

Workflow for biomodalQC, QC workflow for biomodal pipeline

Overview

Dependencies

• biomodalqc 1.0.0

Usage

Cromwell

java -jar cromwell.jar run biomodalQC.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
tag	String	Tag for the biomodal pipeline run
run_name	String	Sequencer run name
library_name	String	Sample library name
lane	String	Sequencer lane number
mode	String	Biomodal pipeline running mode
subsample	String	The target number of reads to subsample for the input fastq file
random_downsample	Boolean	Specify whether use seqtk to choose random reads, if set to false then choose the top reads in fastq
group_desc	String	A text description of what the group ID means
fastqR1	File	Fastq file for read 1
fastqR2	File	Fastq file for read 2

Optional workflow parameters:

Parameter	Value	Default	Description

Optional task parameters:

Parameter	Value	Default	Description
runBiomodalQC.modules	String	"biomodalqc/1.0.0"	Required environment modules
runBiomodalQC.jobMemory	Int	16	Memory allocated for this job (GB)
runBiomodalQC.threads	Int	2	Requested CPU threads
runBiomodalQC.timeout	Int	48	Hours before task timeout

Outputs

Output	Type	Description
dqsreport	File	{'description': 'Html file of QC metric tables and plots', 'vidarr_label': 'dqsreport'}
pipelineSummary	File	{'description': 'csv file of biomodal pipeline summary', 'vidarr_label': 'pipelineSummary'}

Commands

This section lists command(s) run by biomodalQC workflow

• Running biomodalQC

            set -euo pipefail
            
            mkdir init_folder
            ln -s $INIT_FOLDER/* ./init_folder
            cd init_folder

            mkdir -p dataset/~{run_name}/gsi-input
            mkdir -p dataset/~{run_name}/nf-input
            meta_file_path="dataset/~{run_name}/meta_file.csv"
            input_path="dataset/~{run_name}/gsi-input/"
            nf_input_path="dataset/~{run_name}/nf-input/"

            ln -s ~{fastqR1} ${input_path}
            ln -s ~{fastqR2} ${input_path}
            read1_link="${nf_input_path}~{sample_id}_S1_~{lane}_R1_001.fastq.gz"
            read2_link="${nf_input_path}~{sample_id}_S1_~{lane}_R2_001.fastq.gz"
            ln -s ~{fastqR1} ${read1_link}
            ln -s ~{fastqR2} ${read2_link}
            
            cat << EOF > ${meta_file_path}
                sample_id, ~{sample_id}
                description, ~{group_desc}
            EOF

            
            cat << EOF > ./input_config.txt
            tag=~{tag}
            run_name=~{run_name}
            sample_id=~{sample_id}
            lane=~{lane}
            mode=~{mode}
            subsample=~{subsample}
            random_downsample=~{random_downsample}
            meta_file=${meta_file_path}
            data_path=${input_path}
            run_directory=~{run_name}
            work_dir="dataset"
            EOF
            
            ./run_biomodal_qc.sh ./input_config.txt
            cp dataset/~{run_name}/nf-result/duet-1.1.2_~{tag}_~{mode}/dqsreport/~{sample_id}_dqsummary.html ../
            cp dataset/~{run_name}/nf-result/duet-1.1.2_~{tag}_~{mode}/pipeline_report/~{run_name}_~{mode}_Summary.csv ../
            mv ../~{run_name}_~{mode}_Summary.csv ../~{sample_id}_~{mode}_Summary.csv
            chmod -R 770 ./

Support

For support, please file an issue on the Github project or send an email to [email protected] .

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