diff --git a/conf/test_full.config b/conf/test_full.config index d63a1f676..4164903fb 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -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 +}