From 70c1cdbfb0e8ada48556a859286f3828f9ba61c8 Mon Sep 17 00:00:00 2001 From: darrelln32 Date: Mon, 30 Oct 2023 00:11:10 -0400 Subject: [PATCH] Update LaunchMetrics.py put back ChIPSeq and AmpliconSeq recipes for DRAGEN. took out id01. needs an updated RNA hash table for GRCm39 --- scripts/LaunchMetrics.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py index cfa4bc7..f5d8018 100644 --- a/scripts/LaunchMetrics.py +++ b/scripts/LaunchMetrics.py @@ -15,7 +15,7 @@ # Global Variable : we do not want to process these experiments in this script DO_NOT_PROCESS = ["10X_Genomics", "DLP"] # These recipes will be evaluated using DRAGEN because of their larger size of fastqs -RUN_ON_DRAGEN = ["MissionBio", "SingleCellCNV", "MouseWholeGenome", "HumanWholeGenome", "PombeWholeGenome"] +RUN_ON_DRAGEN = ["MissionBio", "SingleCellCNV", "MouseWholeGenome", "HumanWholeGenome", "PombeWholeGenome", "ChIPSeq", "AmpliconSeq"] # this list contains the headers of the columns. we will access the data using these listings PICARD_VERSION = "2_23_2" PICARD_JAR = "/igo/home/igo/resources/picard2.23.2/picard.jar " @@ -131,7 +131,7 @@ def rna_alignment_and_metrics(sample, run, sample_parameters, rna_directory, wor launch_dragen_rna = "/opt/edico/bin/dragen -f -r {} --fastq-list {} --fastq-list-sample-id {} -a {} --intermediate-results-dir /staging/temp --enable-map-align true --enable-sort true --enable-bam-indexing true --enable-map-align-output true --output-format BAM --enable-rna true --enable-duplicate-marking true --enable-rna-quantification true --output-file-prefix {} --output-directory {} ".format(rna_path, fastq_list, sample.sample_id, sample_parameters["GTF"], sample.sample_id, rna_directory) - bsub_launch_dragen_rna = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 48 -M 4 {3}".format(rna_dragen_job_name_header, sample.sample_id, rna_directory, launch_dragen_rna) + bsub_launch_dragen_rna = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id02 id03\" -q dragen -n 48 -M 4 {3}".format(rna_dragen_job_name_header, sample.sample_id, rna_directory, launch_dragen_rna) print(bsub_launch_dragen_rna) call(bsub_launch_dragen_rna, shell = True) @@ -166,7 +166,7 @@ def dragen(sample, run, sample_parameters, work_directory, dragen_directory, fas metric_file_prefix = "{}___P{}___{}___{}".format(run, sample.project[8:], sample.sample_id, sample_parameters["GTAG"]) launch_dragen = "/opt/edico/bin/dragen --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id) - bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_job_name_header, sample.sample_id, dragen_directory, launch_dragen) + bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_job_name_header, sample.sample_id, dragen_directory, launch_dragen) print(bsub_launch_dragen) call(bsub_launch_dragen, shell = True) @@ -209,7 +209,7 @@ def dragen_methylation(sample, run, sample_parameters, work_directory, dragen_di metric_file_prefix = "{}___P{}___{}___{}".format(run, sample.project[8:], sample.sample_id, sample_parameters["GTAG"]) launch_dragen_methylation = "/opt/edico/bin/dragen --enable-methylation-calling true --methylation-protocol directional --ref-dir {} --fastq-list {} --fastq-list-sample-id {} --intermediate-results-dir /staging/temp --output-directory {} --output-file-prefix {} --enable-sort true --enable-duplicate-marking true".format(dragen_path, fastq_list, sample.sample_id, dragen_directory, sample.sample_id) - bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id01 id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_methylation_job_name_header, sample.sample_id, dragen_directory, launch_dragen_methylation) + bsub_launch_dragen = "bsub -J {0}{1} -o {0}{1}.out -cwd \"{2}\" -m \"id02 id03\" -q dragen -n 48 -M 4 {3}".format(dragen_methylation_job_name_header, sample.sample_id, dragen_directory, launch_dragen_methylation) print(bsub_launch_dragen) call(bsub_launch_dragen, shell = True)