v2.9

patidarr · Aug 9, 2017 · ad82f47 · ad82f47
1 parent cda7c7f
commit ad82f47
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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"	: "v2.9dev",
-	"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"	: "v2.9",
+	"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/ruleBook/verifyBamID.rules b/ruleBook/verifyBamID.rules
@@ -1,4 +1,4 @@
-#TARGET     += ["{subject}/{TIME}/{sample}/verifyBamID/{sample}.selfSM".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
+TARGET     += ["{subject}/{TIME}/{sample}/verifyBamID/{sample}.selfSM".format(TIME=TIME, subject=SAMPLE_TO_SUBJECT[s], sample=s) for s in SAMPLES]
 conPair ={}
 if len(config['sample_references']) > 0:
 	for Tumor in config['sample_references']:

diff --git a/submit_snakemake.sh b/submit_snakemake.sh
@@ -58,8 +58,8 @@ fi
 export ACT_DIR="/Actionable/"
 SNAKEFILE=$NGS_PIPELINE/ngs_pipeline.rules
 
-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"