commands.txt

## 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 ./
```