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nextflow.config
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nextflow.config
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/* Define the target files
* and other params
* nextflow run <file.nf> -with-report <report_name>.html -with-trace -with-dag -with-timeline
*/
process {
executor='pbspro'
queue='workq'
cpus = 4
memory = 16.GB
time = 48.h
withLabel: fastqc_raw {
cpus = 3
memory = 4.GB
time = 8.h
}
withLabel: fastp {
cpus = 4
memory = 4.GB
time = 8.h
}
withLabel: fastqc_fastp {
cpus = 3
memory = 4.GB
time = 8.h
}
withLabel: sortmerna {
cpus = 8
memory = 32.GB
time = 30.h
}
withLabel: repair_fastqc {
cpus = 3
memory = 4.GB
time = 4.h
}
withLabel: repair {
cpus = 4
memory = 16.GB
time = 24.h
}
withLabel: star_align {
cpus = 8
memory = 32.GB
time = 4.h
}
withLabel: qualimap {
cpus = 4
memory = 16.GB
time = 4.h
}
withLabel: picard_matrix {
cpus = 4
memory = 8.GB
time = 4.h
}
withLabel: samtools_index {
cpus = 5
memory = 4.GB
time = 4.h
}
withLabel: samtools_flagstat {
cpus = 6
memory = 4.GB
time = 4.h
}
withLabel: featureCounts {
cpus = 6
memory = 8.GB
time = 4.h
}
withLabel: multiqc_repair_fastqc {
cpus = 1
memory = 2.GB
time = 1.h
}
withLabel: multiqc_featureCounts {
cpus = 1
memory = 2.GB
time = 1.h
}
withLabel: multiqc_samtools_flagstat {
cpus = 1
memory = 2.GB
time = 1.h
}
withLabel: multiqc_qualimap {
cpus = 1
memory = 2.GB
time = 1.h
}
withLabel: multiqc_fastp {
cpus = 1
memory = 2.GB
time = 1.h
}
withLabel: multiqc_fastqc_raw {
cpus = 1
memory = 2.GB
time = 1.h
}
withLabel: multiqc_fastqc_fastp {
cpus = 1
memory = 2.GB
time = 1.h
}
withLabel: multiqc_salmon_quant {
cpus = 1
memory = 2.GB
time = 1.h
}
}