Adds bwa -k 23 and GenomeChronicler as tool (#16)

- [x] Adds -k 23 (bwa mem seed length) - [x] Exposes as params bwa_cpus, sort_cpus - [x] Adds GenomeChronicler in tools (sarek logic)
cgpu · Jan 10, 2020 · d1e60c2 · d1e60c2
1 parent bd2c4bb
commit d1e60c2
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Showing 2 changed files with 12 additions and 8 deletions.
diff --git a/main.nf b/main.nf
@@ -51,7 +51,7 @@ def helpMessage() {
                                     Available: Mapping, Recalibrate, VariantCalling, Annotate
                                     Default: Mapping
         --tools                     Specify tools to use for variant calling:
-                                    Available: ASCAT, ControlFREEC, FreeBayes, HaplotypeCaller
+                                    Available: ASCAT, ControlFREEC, FreeBayes, HaplotypeCaller, GenomeChronicler
                                     Manta, mpileup, Mutect2, Strelka, TIDDIT
                                     and/or for annotation:
                                     snpEff, VEP, merge
@@ -797,13 +797,13 @@ process MapReads {
     input = hasExtension(inputFile1, "bam") ? "-p /dev/stdin - 2> >(tee ${inputFile1}.bwa.stderr.log >&2)" : "${inputFile1} ${inputFile2}"
     // Pseudo-code: Add soft-coded memory allocation to the two tools, bwa mem | smatools sort
     // Request only one from the user, the other is implicit: 1 - defined
-    bwa_cpus  = Math.floor ( params.bwa_cpus_fraction * task.cpus) as Integer
-    sort_cpus = task.cpus - bwa_cpus
+    bwa_cpus  = params.bwa_cpus  ? params.bwa_cpus  : Math.floor ( params.bwa_cpus_fraction * task.cpus) as Integer
+    sort_cpus = params.sort_cpus ? params.sort_cpus : task.cpus - bwa_cpus
     """
         ${convertToFastq}
-        bwa mem -K 100000000 -R \"${readGroup}\" ${extra} -t ${task.cpus} -M ${fasta} ${input} > tmp.sam
-        samtools view --threads ${task.cpus} -S -b tmp.sam > unsorted.bam && rm tmp.sam
-        samtools sort --threads ${task.cpus} unsorted.bam -o ${idSample}_${idRun}.bam && rm unsorted.bam
+        bwa mem -k 23 -K 100000000 -R \"${readGroup}\" ${extra} -t ${bwa_cpus} -M ${fasta} \
+        ${input} | \
+        samtools sort --threads ${sort_cpus}  - > ${idSample}_${idRun}.bam
     """
 }
 
@@ -1056,7 +1056,6 @@ process BaseRecalibrator {
     label 'med_resources'
 
     tag {idPatient + "-" + idSample + "-" + intervalBed.baseName}
-    echo true
 
     input:
         set idPatient, idSample, file(bam), file(bai), file(intervalBed) from bamBaseRecalibrator
@@ -1345,6 +1344,8 @@ process RunGenomeChronicler {
   output:
   file("results_${bam.simpleName}") into chronicler_results
 
+  when: 'genomechronicler' in tools
+
   script:
 
   optional_argument = vep.endsWith("no_vepFile.txt") ? '' : "--vepFile ${vep}"
@@ -3351,7 +3352,8 @@ def defineToolList() {
         'strelka',
         'tiddit',
         'tnscope',
-        'vep'
+        'vep',
+        'genomechronicler'
     ]
 }
 

diff --git a/nextflow.config b/nextflow.config
@@ -77,6 +77,8 @@ params {
   med_resources_fraction = 0.50
   singleCPUMem = 7.GB
   bwa_cpus_fraction   = 0.6
+  bwa_cpus = null
+  sort_cpus = null
 
   // Deprecated params
   annotateVCF = null