v2.8

patidarr · Jun 6, 2017 · e886927 · e886927
1 parent caa5115
commit e886927
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Showing 3 changed files with 6 additions and 6 deletions.
diff --git a/config/config_common.json b/config/config_common.json
@@ -1,7 +1,7 @@
 {
-	"pipeline_version"	: "v2.7",
-	"mail"			: "-c patidarr@mail.nih.gov",
-	"mails"			: "-c patidarr@mail.nih.gov -c manoj.tyagi@nih.gov -c wangc@mail.nih.gov -c yujin.lee@nih.gov -c NCIBioinformatics_Oncogenomics@mail.nih.gov",
+	"pipeline_version"	: "v2.8",
+	"mails"			: "-c patidarr@mail.nih.gov",
+	"mail"			: "-c patidarr@mail.nih.gov -c manoj.tyagi@nih.gov -c wangc@mail.nih.gov -c yujin.lee@nih.gov -c NCIBioinformatics_Oncogenomics@mail.nih.gov",
 	"platform"		: "Illumina",
 	"samtools"		: "0.1.19",
 	"samtools_old"		: "0.1.19",

diff --git a/ngs_pipeline.snakefile b/ngs_pipeline.snakefile
@@ -130,7 +130,7 @@ for subject  in config['RNASeq'].keys():
 ALL_FASTQC  = ["{subject}/{TIME}/{sample}/qc/fastqc/{sample}_R2_fastqc.html".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC      = ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.flagstat.txt".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC     += ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.squeeze.done".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
-#ALL_QC     += ["{subject}/{TIME}/{sample}/verifyBamID/{sample}.selfSM".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
+ALL_QC     += ["{subject}/{TIME}/{sample}/verifyBamID/{sample}.selfSM".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC     += ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.hotspot.depth".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 ALL_QC     += ["{subject}/{TIME}/{sample}/qc/{sample}.bwa.gt".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 #ALL_QC     += ["{subject}/{TIME}/{sample}/qc/BamQC/qualimapReport.html".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]

diff --git a/submit_snakemake.sh b/submit_snakemake.sh
@@ -59,8 +59,8 @@ fi
 export ACT_DIR="/Actionable/"
 SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.snakefile
 
-cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R RNASeq "
-#cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R makeConfig RNASeq "
+#cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R RNASeq "
+cmd="--directory $WORK_DIR --snakefile $SNAKEFILE --configfile $SAM_CONFIG --jobscript $NGS_PIPELINE/scripts/jobscript.sh --jobname {params.rulename}.{jobid} --nolock  --ri -k -p -T -r -j 3000 --resources DeFuse=25 --resources SIFT=8 --stats ngs_pipeline_${NOW}.stats -R makeConfig RNASeq "
 umask 022
 if [ $HOST   == 'biowulf.nih.gov' ]; then
 	echo "Host identified as $HOST"