merging json files

CCBR · Nov 1, 2018 · 68d45f1 · 68d45f1
2 parents e14d71a + 687ceba
commit 68d45f1
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Showing 9 changed files with 864 additions and 9 deletions.
diff --git a/Rules/ChIPseq.snakefile b/Rules/ChIPseq.snakefile
@@ -63,7 +63,7 @@ pipehome = config['project']['pipehome']
 
 print(pipehome)
 
-include: join(pipehome, "Rules", "InitialChIPseqQC.snakefile")
+#include: join(pipehome, "Rules", "InitialChIPseqQC.snakefile")
 
 bam_suffix = '.sorted.bam'
 #####################

diff --git a/Rules/gatk.splitncigarreads.rl b/Rules/gatk.splitncigarreads.rl
@@ -2,4 +2,4 @@ rule gatk_splitcigar:
       input:  "{x}.dedup_unsplit.bam"
       output: temp("{x}.dedup.bam")
       params: gatk=config['bin'][pfamily]['GATK'],genome=config['references'][pfamily]['GENOME'],rname="pl:split"
-      shell:  "module load GATK/3.7; GATK -m 64g SplitNCigarReads -I {input} -R {params.genome} -o {output} -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS"
+      shell:  "module load GATK/3.8-0; GATK -m 64g SplitNCigarReads -I {input} -R {params.genome} -o {output} -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS"