From e8869272fab94869130e03e67e830a5ac07ed3fb Mon Sep 17 00:00:00 2001 From: patidarr Date: Tue, 6 Jun 2017 11:09:30 -0400 Subject: [PATCH] v2.8 --- config/config_common.json | 6 +++--- ngs_pipeline.snakefile | 2 +- submit_snakemake.sh | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/config/config_common.json b/config/config_common.json index 1d0f839..aa1a993 100644 --- 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 index 2d61401..0e4ba68 100644 --- 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 index 8cf01c1..d37a5c7 100644 --- 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"