Housekeeping

conf/modules.config

@@ -403,7 +403,7 @@ process {
             pattern: "*cram"
         ]
     }
-    withName: 'QUALIMAP_BAMQC_CRAM' {
+    withName: 'QUALIMAP_BAMQCCRAM' {
         ext.args         = '--paint-chromosome-limits --genome-gc-distr HUMAN -skip-duplicated --skip-dup-mode 0 -outformat HTML'
         ext.prefix       = { "${meta.id}.recal" }
         ext.when         = { !(params.skip_tools && params.skip_tools.contains('bamqc')) }

modules.json

@@ -10,13 +10,13 @@
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "bwa/mem": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "950700bcdc0e9a2b6883d40d2c51c6fc435cd714"
             },
             "bwamem2/index": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "bwamem2/mem": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "950700bcdc0e9a2b6883d40d2c51c6fc435cd714"
             },
             "cat/fastq": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -27,8 +27,11 @@
             "custom/dumpsoftwareversions": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "deeptools/bamcoverage": {
+                "git_sha": "fdb1664885480d9411c24ba45bb4fde4738e5907"
+            },
             "deepvariant": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "c450b08a75cda8878876ccbbe42493d6774397bd"
             },
             "ensemblvep": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
@@ -72,6 +75,9 @@
             "gatk4/gatherbqsrreports": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "gatk4/gatherpileupsummaries": {
+                "git_sha": "8c8be7d7c6c5b17b89f1c392866fc433b0f79d69"
+            },
             "gatk4/genomicsdbimport": {
                 "git_sha": "967fb22dedc2c8855f00e64c3d7b5814c85242a6"
             },
@@ -84,12 +90,18 @@
             "gatk4/haplotypecaller": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "gatk4/intervallisttobed": {
+                "git_sha": "fcd483e1b5156262a60184d96e7cd35d8d475bf4"
+            },
             "gatk4/learnreadorientationmodel": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "gatk4/markduplicates": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "gatk4/mergemutectstats": {
+                "git_sha": "3f364e2f31443f6742e8c63bf2083b5583431ef7"
+            },
             "gatk4/mutect2": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
@@ -114,29 +126,35 @@
             "multiqc": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
+            "qualimap/bamqc": {
+                "git_sha": "e31f1ff3b1375b30db08637d8937e25cc046f3cc"
+            },
+            "qualimap/bamqccram": {
+                "git_sha": "950700bcdc0e9a2b6883d40d2c51c6fc435cd714"
+            },
             "samblaster": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
             },
             "samtools/bam2fq": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
             },
             "samtools/faidx": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
             },
             "samtools/index": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
             },
             "samtools/merge": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
             },
             "samtools/mpileup": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
             },
             "samtools/stats": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
             },
             "samtools/view": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+                "git_sha": "1ad73f1b2abdea9398680d6d20014838135c9a35"
             },
             "seqkit/split2": {
                 "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"

modules/local/gatk4/markduplicatesspark/main.nf

@@ -2,13 +2,13 @@ process GATK4_MARKDUPLICATES_SPARK {
     tag "$meta.id"
     label 'process_high'
 
-    conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null)
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' :
-        'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' :
+        'broadinstitute/gatk:4.2.5.0' }"
 
     input:
-    tuple val(meta), path(bam)
+    tuple val(meta), path(bams)
     path  fasta
     path  fasta_fai
     path  dict
@@ -21,23 +21,23 @@ process GATK4_MARKDUPLICATES_SPARK {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args  ?: ''
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def bam_list = bams.collect(){ bam -> "-I ".concat(bam.toString()) }.join(" ")
     def avail_mem = 3
     if (!task.memory) {
         log.info '[GATK MarkDuplicatesSpark] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
     } else {
         avail_mem = task.memory.giga
     }
-    prefix = task.ext.prefix ?: "${meta.id}"
-    def bams = bam.collect(){ x -> "-I ".concat(x.toString()) }.join(" ")
     """
-    gatk  \
-        MarkDuplicatesSpark \
-        $bams \
-        -O ${prefix} \
-        --reference ${fasta} \
-        --tmp-dir . \
+    export SPARK_USER=spark3
+    gatk --java-options "-Xmx${avail_mem}g" MarkDuplicatesSpark \\
         --spark-master local[${task.cpus}] \\
+        $bam_list \\
+        --reference ${fasta} \\
+        --tmp-dir . \\
+        --output ${prefix} \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -46,3 +46,9 @@ process GATK4_MARKDUPLICATES_SPARK {
     END_VERSIONS
     """
 }
+
+//export SPARK_LOCAL_IP=127.0.0.1
+    // export SPARK_PUBLIC_DNS=127.0.0.1
+        // --conf spark.jars.ivy=/tmp/.ivy \\
+// export SPARK_USER=spark3
+//--conf 'spark.kryo.referenceTracking=false' \\