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rest-test-data.json
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{
"data": {
"global": [{
"indir": "R_151215_YOUIDA_M001_pt1of7"
},
{
"outdir": "R_151215_YOUIDA_M001_pt1of7/processed"
},
{
"file_rule": "(15.*)$"
},
{
"by_sample_outdir": 1
},
{
"find_by_dir": 1
},
{
"wait": 0
},
{
"trimmomatic_dir": "R_151215_YOUIDA_M001_pt1of7/processed/{$sample}/trimmomatic"
},
{
"trimmomatic": "R_151215_YOUIDA_M001_pt1of7/processed/{$sample}/trimmomatic"
},
{
"raw_fastqc_dir": "R_151215_YOUIDA_M001_pt1of7/processed/{$sample}"
},
{
"raw_fastqc": "R_151215_YOUIDA_M001_pt1of7/processed/{$sample}"
},
{
"analysis_dir": "R_151215_YOUIDA_M001_pt1of7/processed/analysis"
},
{
"READ1": "{$self->raw_fastqc_dir}/raw_fastqc/{$sample}_read1.fastq.gz"
},
{
"READ2": "{$self->raw_fastqc_dir}/raw_fastqc/{$sample}_read2.fastq.gz"
},
{
"TR1": "{$self->trimmomatic_dir}/{$sample}_read1_trimmomatic"
},
{
"TR2": "{$self->trimmomatic_dir}/{$sample}_read2_trimmomatic"
}
],
"rules": [{
"raw_fastqc": {
"local": [{
"CAT1": "{$self->indir}/*_R1*.fastq.gz"
},
{
"CAT2": "{$self->indir}/*_R1*.fastq.gz"
},
{
"before_meta": "HPC Directives\n\n#\n#HPC jobname=raw_fastqc\n#HPC module=gencore/1 gencore_dev gencore_qc\n#HPC ntasks=1\n#HPC procs=1\n#HPC commands_per_node=1\n#HPC mem=12GB\n#HPC walltime=01:00:00\n#HPC cpus_per_task=3\n#HPC partition=serial\n"
}
],
"process": "#TASK tags={$sample}_R1\n#mkdir -p {$self->{outdir}}/{$sample}_R1_FASTQC && \\\n# cat {$self->CAT1} > {$self->READ1} && \\\n# fastqc --extract \\\n# {$self->READ1} \\\n# -o {$self->{outdir}}/{$sample}_R1_FASTQC/ -t 3\n\n#TASK tags={$sample}_R2\n#mkdir -p {$self->{outdir}}/{$sample}_R2_FASTQC && \\\n# cat {$self->CAT2} > {$self->READ2} && \\\n# fastqc --extract \\\n# {$self->READ2} \\\n# -o {$self->{outdir}}/{$sample}_R2_FASTQC/ -t 3\n"
}
},
{
"trimmomatic": {
"local": [{
"before_meta": "HPC Directives\n\n#\n#HPC jobname=trimmomatic\n#HPC module=gencore/1 gencore_dev gencore_qc\n#HPC mem=25GB\n#HPC walltime=48:00:00\n#HPC cpus_per_task=12\n#HPC ntasks=1\n#HPC procs=1\n#HPC commands_per_node=1\n#HPC partition=serial\n#\n"
}],
"process": "#TASK tags={$sample}\ntrimmomatic \\\n PE -threads 12 \\\n -trimlog {$self->outdir}/{$sample}_trimmomatic.log \\\n {$self->READ1} \\\n {$self->READ2} \\\n {$self->TR1}_1PE.fastq \\\n {$self->TR1}_1SE.fastq \\\n {$self->TR2}_2PE.fastq \\\n {$self->TR2}_2SE.fastq \\\n TRAILING:3 LEADING:3 SLIDINGWINDOW:4:15 MINLEN:36\n"
}
},
{
"trimmomatic_fastqc": {
"local": [{
"OUTPUT": "{$self->outdir}/{$sample}"
},
{
"before_meta": "HPC Directives\n\n#\n#HPC jobname=trimmomatic_fastqc\n#HPC deps=trimmomatic\n#HPC module=gencore/1 gencore_dev gencore_qc\n#HPC mem=12GB\n#HPC ntasks=1\n#HPC procs=1\n#HPC commands_per_node=1\n#HPC walltime=20:00:00\n#HPC cpus_per_task=4\n#HPC partition=serial\n#\n"
}
],
"process": "#TASK tags={$sample}\nmkdir -p {$self->OUTPUT}_FASTQC_read1_TRIMMED && \\\n fastqc --extract \\\n {$self->TR1}_1PE.fastq \\\n -o {$self->OUTPUT}_FASTQC_read1_TRIMMED/ -t 4\n\n#TASK tags={$sample}\nmkdir -p {$self->OUTPUT}_FASTQC_read2_TRIMMED && \\\n fastqc --extract \\\n {$self->TR2}_2PE.fastq \\\n -o {$self->OUTPUT}_FASTQC_read2_TRIMMED/ -t 4\n"
}
},
{
"trimmomatic_gzip": {
"local": [{
"indir": "{$self->trimmomatic}"
},
{
"INPUT": "{$self->trimmomatic}/{$sample}"
},
{
"before_meta": "HPC Directives\n\n#\n#HPC jobname=trimmomatic_gzip\n#HPC deps=trimmomatic\n#HPC mem=10GB\n#HPC module=gencore/1 gencore_dev gencore_qc\n#HPC walltime=12:30:00\n#HPC cpus_per_task=1\n#HPC commands_per_node=1\n#HPC partition=serial\n#\n"
}
],
"process": "#TASK tags={$sample}\ngzip -f {$self->TR1}_1PE.fastq\n\n#TASK tags={$sample}\ngzip -f {$self->TR2}_2PE.fastq\n"
}
},
{
"remove_trimmomatic_logs": {
"local": [{
"create_outdir": 0
},
{
"before_meta": "HPC Directives\n\n#\n#HPC jobname=remove_trimmomatic_logs\n#HPC deps=trimmomatic\n#HPC module=gencore/1 gencore_dev gencore_qc\n#HPC mem=4GB\n#HPC walltime=00:20:00\n#HPC cpus_per_task=1\n#HPC commands_per_node=1\n#HPC partition=serial\n#\n"
}
],
"process": "#TASK tags={$sample}\nfind {$self->trimmomatic_dir} -name \"*_trimmomatic.log\" -type f -delete\n"
}
}
]
}
}