Commit ea66eb10 authored by Tamara Hodgetts's avatar Tamara Hodgetts
Browse files

Merge branch 'resource-allocation' into dev

parents 2cea0207 9a363007

conf/resources.config

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/*

========================================================================================

    nf-core/cutandrun Nextflow resource config file

========================================================================================

    Minimal and process-specific resource allocation.

----------------------------------------------------------------------------------------

*/



/*

========================================================================================

    MINIMAL AND ULTRA LOW RESOURCE ALLOCATION

========================================================================================

*/



process {

    withLabel:process_min {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }

    

    withLabel:process_ultralow {

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }

}



/*

========================================================================================

    MODULE-SPECIFIC RESOURCE ALLOCATION

========================================================================================

*/



process {

    withName: '.*:ALIGN_BOWTIE2:BOWTIE2_ALIGN' {

        cpus   = { check_max( 32     * task.attempt, 'cpus'    ) }

        memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h    * task.attempt, 'time'    ) }

    }

    

    withName: '.*:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN' {

        cpus   = { check_max( 32     * task.attempt, 'cpus'    ) }

        memory = { check_max( 64.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h    * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_GENE' {

        cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }

        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h    * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_COMPUTEMATRIX_PEAKS' {

        cpus   = { check_max( 16     * task.attempt, 'cpus'    ) }

        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h    * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:CUSTOM_DUMPSOFTWAREVERSIONS' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_INDEX' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_STATS' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_STATS' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_IDXSTATS' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_FLAGSTAT' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }



    withName: '.*CHROMSIZES' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 2.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 1.h   * task.attempt, 'time'    ) }

    }



    // 1 CPU 8 GB

    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_GENOMECOV' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:BEDTOOLS_SORT' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDGRAPHTOBIGWIG' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:BEDTOOLS_INTERSECT' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: '.*:CONSENSUS_PEAKS:BEDTOOLS_MERGE|.*:CONSENSUS_PEAKS_ALL:BEDTOOLS_MERGE' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_PEAKCALLING:UCSC_BEDCLIP' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    // ultralow

    withName: '.*:CALCULATE_FRAGMENTS:BEDTOOLS_BAMTOBED' {

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:SEACR_CALLPEAK' {

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC' {

        cpus   = { check_max( 2     * task.attempt, 'cpus'    ) }

        memory = { check_max( 8.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    // memory

    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:DEEPTOOLS_PLOTHEATMAP_PEAKS' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }



    withName: 'NFCORE_CUTANDRUN:CUTANDRUN:.*:SAMTOOLS_VIEW' {

        cpus   = { check_max( 1     * task.attempt, 'cpus'    ) }

        memory = { check_max( 32.GB  * task.attempt, 'memory'  ) }

        time   = { check_max( 4.h   * task.attempt, 'time'    ) }

    }

}
 
 No newline at end of file

modules/local/export_meta.nf

+1 −1
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process EXPORT_META {

    label 'process_low'

    label 'process_min'



    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/linux/awk.nf

+1 −1
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process AWK {

    tag "$meta.id"

    label 'process_low'

    label 'process_ultralow'



    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/linux/awk_script.nf

+1 −1
Original line number Diff line number Diff line 
process AWK_SCRIPT {

    tag "$meta.id"

    label 'process_low'

    label 'process_min'



    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

modules/local/linux/cut.nf

+1 −1
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process CUT {

    tag "$meta.id"

    label 'process_low'

    label 'process_min'



    conda (params.enable_conda ? "conda-forge::gawk=5.1.0" : null)

    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?

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