Add memory stuff to all gatk4 modules (#1122)

* Add memory stuff to all gatj4 modules * Add removed input line back in * revert script section
2024-09-20 23:32:05 +00:00 · 2021-12-07 15:22:24 +01:00 · 2021-12-07 15:22:24 +01:00 · 7389963d5c
commit 7389963d5c
parent d473a247d2
23 changed files with 129 additions and 26 deletions
--- a/modules/gatk4/applybqsr/main.nf
+++ b/modules/gatk4/applybqsr/main.nf
@ -22,13 +22,14 @@ process GATK4_APPLYBQSR {
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def interval = intervals ? "-L ${intervals}" : ""
+    def avail_mem = 3
    if (!task.memory) {
        log.info '[GATK ApplyBQSR] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
    """
-    gatk ApplyBQSR \\
+    gatk --java-options "-Xmx${avail_mem}g" ApplyBQSR \\
        -R $fasta \\
        -I $input \\
        --bqsr-recal-file $bqsr_table \\
--- a/modules/gatk4/baserecalibrator/main.nf
+++ b/modules/gatk4/baserecalibrator/main.nf
@ -25,14 +25,14 @@ process GATK4_BASERECALIBRATOR {
    def prefix = task.ext.prefix ?: "${meta.id}"
    def intervalsCommand = intervalsBed ? "-L ${intervalsBed}" : ""
    def sitesCommand = knownSites.collect{"--known-sites ${it}"}.join(' ')
-
+    def avail_mem = 3
    if (!task.memory) {
        log.info '[GATK BaseRecalibrator] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
    """
-    gatk BaseRecalibrator  \
+    gatk --java-options "-Xmx${avail_mem}g" BaseRecalibrator  \
        -R $fasta \
        -I $input \
        $sitesCommand \
--- a/modules/gatk4/bedtointervallist/main.nf
+++ b/modules/gatk4/bedtointervallist/main.nf
@ -18,8 +18,14 @@ process GATK4_BEDTOINTERVALLIST {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK BedToIntervalList] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk BedToIntervalList \\
+    gatk --java-options "-Xmx${avail_mem}g" BedToIntervalList \\
        -I $bed \\
        -SD $sequence_dict \\
        -O ${prefix}.interval_list \\
--- a/modules/gatk4/calculatecontamination/main.nf
+++ b/modules/gatk4/calculatecontamination/main.nf
@ -21,8 +21,14 @@ process GATK4_CALCULATECONTAMINATION {
    def prefix = task.ext.prefix ?: "${meta.id}"
    def matched_command = matched ? " -matched ${matched} " : ''
    def segment_command = segmentout ? " -segments ${prefix}.segmentation.table" : ''
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK CalculateContamination] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk CalculateContamination \\
+    gatk --java-options "-Xmx${avail_mem}g" CalculateContamination \\
        -I $pileup \\
        $matched_command \\
        -O ${prefix}.contamination.table \\
--- a/modules/gatk4/createsequencedictionary/main.nf
+++ b/modules/gatk4/createsequencedictionary/main.nf
@ -18,7 +18,7 @@ process GATK4_CREATESEQUENCEDICTIONARY {
    def args = task.ext.args ?: ''
    def avail_mem = 6
    if (!task.memory) {
-        log.info '[GATK] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
+        log.info '[GATK CreateSequenceDictionary] Available memory not known - defaulting to 6GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
--- a/modules/gatk4/createsomaticpanelofnormals/main.nf
+++ b/modules/gatk4/createsomaticpanelofnormals/main.nf
@ -21,8 +21,14 @@ process GATK4_CREATESOMATICPANELOFNORMALS {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK CreateSomaticPanelOfNormals] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk \\
+    gatk --java-options "-Xmx${avail_mem}g" \\
        CreateSomaticPanelOfNormals \\
        -R $fasta \\
        -V gendb://$genomicsdb \\
--- a/modules/gatk4/estimatelibrarycomplexity/main.nf
+++ b/modules/gatk4/estimatelibrarycomplexity/main.nf
@ -29,7 +29,7 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY {
        avail_mem = task.memory.giga
    }
    """
-    gatk EstimateLibraryComplexity \
+    gatk --java-options "-Xmx${avail_mem}g" EstimateLibraryComplexity \
        ${crams} \
        -O ${prefix}.metrics \
        --REFERENCE_SEQUENCE ${fasta} \
--- a/modules/gatk4/fastqtosam/main.nf
+++ b/modules/gatk4/fastqtosam/main.nf
@ -18,8 +18,14 @@ process GATK4_FASTQTOSAM {
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def read_files = meta.single_end ? "-F1 $reads" : "-F1 ${reads[0]} -F2 ${reads[1]}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK FastqToSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk FastqToSam \\
+    gatk --java-options "-Xmx${avail_mem}g" FastqToSam \\
        $read_files \\
        -O ${prefix}.bam \\
        -SM $prefix \\
--- a/modules/gatk4/filtermutectcalls/main.nf
+++ b/modules/gatk4/filtermutectcalls/main.nf
@ -37,8 +37,14 @@ process GATK4_FILTERMUTECTCALLS {
    if (contaminationfile) {
        contamination_options = '--contamination-table ' + contaminationfile.join(' --contamination-table ')
    }
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK FilterMutectCalls] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk FilterMutectCalls \\
+    gatk --java-options "-Xmx${avail_mem}g" FilterMutectCalls \\
        -R $fasta \\
        -V $vcf \\
        $orientationbias_options \\
--- a/modules/gatk4/genomicsdbimport/main.nf
+++ b/modules/gatk4/genomicsdbimport/main.nf
@ -42,8 +42,14 @@ process GATK4_GENOMICSDBIMPORT {
        updated_db = wspace.toString()
    }

+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK GenomicsDBImport] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk GenomicsDBImport \\
+    gatk --java-options "-Xmx${avail_mem}g" GenomicsDBImport \\
        $inputs_command \\
        $dir_command \\
        $intervals_command \\
--- a/modules/gatk4/genotypegvcfs/main.nf
+++ b/modules/gatk4/genotypegvcfs/main.nf
@ -26,8 +26,14 @@ process GATK4_GENOTYPEGVCFS {
    def dbsnp_options    = dbsnp ? "-D ${dbsnp}" : ""
    def interval_options = intervals_bed ? "-L ${intervals_bed}" : ""
    def gvcf_options     = gvcf.name.endsWith(".vcf") || gvcf.name.endsWith(".vcf.gz") ? "$gvcf" : "gendb://$gvcf"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK GenotypeGVCFs] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk \\
+    gatk --java-options "-Xmx${avail_mem}g" \\
        GenotypeGVCFs \\
        $args \\
        $interval_options \\
--- a/modules/gatk4/getpileupsummaries/main.nf
+++ b/modules/gatk4/getpileupsummaries/main.nf
@ -24,8 +24,14 @@ process GATK4_GETPILEUPSUMMARIES {

    sitesCommand = sites ? " -L ${sites} " : " -L ${variants} "

+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK GetPileupSummaries] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk GetPileupSummaries \\
+    gatk --java-options "-Xmx${avail_mem}g" GetPileupSummaries \\
        -I $bam \\
        -V $variants \\
        $sitesCommand \\
--- a/modules/gatk4/indexfeaturefile/main.nf
+++ b/modules/gatk4/indexfeaturefile/main.nf
@ -16,8 +16,14 @@ process GATK4_INDEXFEATUREFILE {

    script:
    def args = task.ext.args ?: ''
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK IndexFeatureFile] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk \\
+    gatk --java-options "-Xmx${avail_mem}g" \\
        IndexFeatureFile \\
        $args \\
        -I $feature_file
--- a/modules/gatk4/intervallisttools/main.nf
+++ b/modules/gatk4/intervallisttools/main.nf
@ -17,11 +17,17 @@ process GATK4_INTERVALLISTTOOLS {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK IntervalListTools] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """

    mkdir ${prefix}_split

-    gatk \\
+    gatk --java-options "-Xmx${avail_mem}g" \\
        IntervalListTools \\
        -I ${interval_list} \\
        -O ${prefix}_split \\
--- a/modules/gatk4/learnreadorientationmodel/main.nf
+++ b/modules/gatk4/learnreadorientationmodel/main.nf
@ -19,8 +19,14 @@ process GATK4_LEARNREADORIENTATIONMODEL {
    def prefix = task.ext.prefix ?: "${meta.id}"
    def inputs_list = []
    f1r2.each() { a -> inputs_list.add(" -I " + a) }
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK LearnReadOrientationModel] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk \\
+    gatk --java-options "-Xmx${avail_mem}g" \\
        LearnReadOrientationModel \\
        ${inputs_list.join(' ')} \\
        -O ${prefix}.tar.gz \\
--- a/modules/gatk4/markduplicates/main.nf
+++ b/modules/gatk4/markduplicates/main.nf
@ -20,14 +20,14 @@ process GATK4_MARKDUPLICATES {
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def bam_list = bams.collect(){ bam -> "--INPUT ".concat(bam.toString()) }.join(" ")
-    def avail_mem       = 3
+    def avail_mem = 3
    if (!task.memory) {
-        log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+        log.info '[GATK MarkDuplicates] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.giga
    }
    """
-    gatk MarkDuplicates \\
+    gatk --java-options "-Xmx${avail_mem}g" MarkDuplicates \\
        $bam_list \\
        --METRICS_FILE ${prefix}.metrics \\
        --TMP_DIR . \\
--- a/modules/gatk4/mergebamalignment/main.nf
+++ b/modules/gatk4/mergebamalignment/main.nf
@ -20,8 +20,14 @@ process GATK4_MERGEBAMALIGNMENT {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK MergeBamAlignment] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk MergeBamAlignment \\
+    gatk --java-options "-Xmx${avail_mem}g" MergeBamAlignment \\
        ALIGNED=$aligned \\
        UNMAPPED=$unmapped \\
        R=$fasta \\
--- a/modules/gatk4/mergevcfs/main.nf
+++ b/modules/gatk4/mergevcfs/main.nf
@ -26,8 +26,14 @@ process GATK4_MERGEVCFS {
        input += " I=${vcf}"
    }
    def ref = use_ref_dict ? "D=${ref_dict}" : ""
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK MergeVcfs] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk MergeVcfs \\
+    gatk --java-options "-Xmx${avail_mem}g" MergeVcfs \\
        $input \\
        O=${prefix}.vcf.gz \\
        $ref \\
--- a/modules/gatk4/mutect2/main.nf
+++ b/modules/gatk4/mutect2/main.nf
@ -53,8 +53,14 @@ process GATK4_MUTECT2 {
        normals_command = '-normal ' + which_norm.join( ' -normal ')
    }

+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK Mutect2] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk Mutect2 \\
+    gatk --java-options "-Xmx${avail_mem}g" Mutect2 \\
        -R ${fasta} \\
        ${inputs_command} \\
        ${normals_command} \\
--- a/modules/gatk4/revertsam/main.nf
+++ b/modules/gatk4/revertsam/main.nf
@ -17,8 +17,14 @@ process GATK4_REVERTSAM {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK RevertSam] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk RevertSam \\
+    gatk --java-options "-Xmx${avail_mem}g" RevertSam \\
        I=$bam \\
        O=${prefix}.reverted.bam \\
        $args
--- a/modules/gatk4/samtofastq/main.nf
+++ b/modules/gatk4/samtofastq/main.nf
@ -18,8 +18,14 @@ process GATK4_SAMTOFASTQ {
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
    def output   = meta.single_end ? "FASTQ=${prefix}.fastq.gz" : "FASTQ=${prefix}_1.fastq.gz SECOND_END_FASTQ=${prefix}_2.fastq.gz"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK SamToFastq] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk SamToFastq \\
+    gatk --java-options "-Xmx${avail_mem}g" SamToFastq \\
        I=$bam \\
        $output \\
        $args
--- a/modules/gatk4/splitncigarreads/main.nf
+++ b/modules/gatk4/splitncigarreads/main.nf
@ -20,8 +20,14 @@ process GATK4_SPLITNCIGARREADS {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK SplitNCigarReads] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
    """
-    gatk SplitNCigarReads \\
+    gatk --java-options "-Xmx${avail_mem}g" SplitNCigarReads \\
        -R $fasta \\
        -I $bam \\
        -O ${prefix}.bam \\
--- a/modules/gatk4/variantfiltration/main.nf
+++ b/modules/gatk4/variantfiltration/main.nf
@ -23,7 +23,7 @@ process GATK4_VARIANTFILTRATION {
    def prefix = task.ext.prefix ?: "${meta.id}"
    def avail_mem = 3
    if (!task.memory) {
-        log.info '[GATK HaplotypeCaller] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+        log.info '[GATK VariantFiltration] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
    } else {
        avail_mem = task.memory.toGiga()
    }