fixed X11 graphics bug in qualimap

CCBR · Dec 12, 2017 · b45c833 · b45c833
1 parent 8818d0e
commit b45c833
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Showing 2 changed files with 3 additions and 4 deletions.
diff --git a/Rules/qualimap.rl b/Rules/qualimap.rl
@@ -1,8 +1,7 @@
 rule qualimap:
     input:  bam="{x}.dedup.bam",
             bed=config['project']['workpath']+"/exome_targets.bed"
-    output: "QC/{x}.qualimapReport","QC/{x}.qualimapReport/genome_results.txt"
+    output: dir="QC/{x}.qualimapReport",txt="QC/{x}.qualimapReport/genome_results.txt"
     threads: 8
     params: qualimap=config['bin'][pfamily]['QUALIMAP'],organism=config['references'][pfamily]['ORGANISM'],regions="exome_targets.bed",rname="pl:qualimap"
-#    shell:  "{params.qualimap} bamqc -bam {input} -c gd {params.organism} -outfile {output} -gff {params.regions} -outformat HTML -nw 500 -p NON-STRAND-SPECIFIC -nt {threads}"
-    shell:  "module load qualimap/2.2.1; qualimap bamqc --java-mem-size=96G -bam {input.bam} -c gd {params.organism} -ip -outdir {output} -gff {params.regions} -outformat HTML -nt {threads} --skip-duplicated -nw 500 -p NON-STRAND-SPECIFIC"
+    shell:  "{params.qualimap} bamqc -bam {input.bam} -c gd {params.organism} -ip -outdir {output.dir} -gff {params.regions} -outfile report.pdf -outformat PDF -nt {threads} --skip-duplicated -nw 500 -p NON-STRAND-SPECIFIC"
diff --git a/standard-bin.json b/standard-bin.json
@@ -26,7 +26,7 @@
         "SAMTOOLS": "/usr/local/apps/samtools/1.3.1/bin/samtools",
         "BAMTOOLS": "/usr/local/apps/bamtools/2.3.0/bin/bamtools",
         "BEDTOOLS": "/usr/local/apps/bedtools/2.19.0/bin/bedtools",
-        "QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2/qualimap --java-mem-size=64G",
+        "QUALIMAP": "export JAVA_OPTS='-Djava.awt.headless=true -Djava.io.tmpdir=/lscratch/$SLURM_JOBID'; /usr/local/apps/qualimap/qualimap_v2.2.1/qualimap --java-mem-size=96G",
         "STAR": "/usr/local/apps/STAR/2.4.0h/bin/Linux_x86_64/STAR",
         "SNPEFF": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/snpEff.jar",
         "SNPSIFT": "java -Xmx24g -Djava.io.tmpdir=/lscratch/$SLURM_JOBID -jar /usr/local/apps/snpEff/4.2/SnpSift.jar",