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Copy optimized resources from Tower
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@edmundmiller
edmundmiller committed Feb 6, 2024
1 parent a53a004 commit 4ab3ecb
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218 changes: 218 additions & 0 deletions conf/test_full.config
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Expand Up @@ -19,3 +19,221 @@ params {
genome = 'GRCh37'
pseudo_aligner = 'salmon'
}

// Copied from Tower
process {
withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT' {
cpus = { 7 * task.attempt }
memory = { 6.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
cpus = { 6 * task.attempt }
memory = { 36.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES' {
cpus = { 2 * task.attempt }
memory = { 31.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION' {
cpus = { 2 * task.attempt }
memory = { 3.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION' {
cpus = { 2 * task.attempt }
memory = { 2.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION' {
cpus = { 2 * task.attempt }
memory = { 33.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV' {
cpus = { 2 * task.attempt }
memory = { 16.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:CUSTOM_DUMPSOFTWAREVERSIONS' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON' {
cpus = { 3 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:DUPRADAR' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC' {
cpus = { 2 * task.attempt }
memory = { 2.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE' {
cpus = { 8 * task.attempt }
memory = { 7.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:INPUT_CHECK:SAMPLESHEET_CHECK' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:MULTIQC' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:GTF_GENE_FILTER' {
cpus = { 1 * task.attempt }
memory = { 2.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA' {
cpus = { 1 * task.attempt }
memory = { 2.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:PREPARE_GENOME:SALMON_INDEX' {
cpus = { 5 * task.attempt }
memory = { 19.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ' {
cpus = { 1 * task.attempt }
memory = { 10.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_QUANT' {
cpus = { 7 * task.attempt }
memory = { 18.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_LENGTH_SCALED' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE_SCALED' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TX2GENE' {
cpus = { 1 * task.attempt }
memory = { 8.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_SALMON:SALMON_TXIMPORT' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT' {
cpus = { 6 * task.attempt }
memory = { 7.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_LENGTH_SCALED' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_GENE_SCALED' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_SE_TRANSCRIPT' {
cpus = { 2 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TX2GENE' {
cpus = { 1 * task.attempt }
memory = { 8.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_TXIMPORT' {
cpus = { 1 * task.attempt }
memory = { 1.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE' {
cpus = { 2 * task.attempt }
memory = { 2.GB * task.attempt }
}
withName: 'NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS' {
cpus = { 4 * task.attempt }
memory = { 2.GB * task.attempt }
}
errorStrategy = 'retry'
maxRetries = 2
}

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