From c678a47bb3d6b36fdcc00c89aed085355dea86d5 Mon Sep 17 00:00:00 2001 From: darrelln32 Date: Sun, 9 Apr 2023 13:33:42 -0400 Subject: [PATCH] Update alignment_and_picard.py had to remove the hardcoded gtf_file variable because that gtf file points to the human annotation file. if there is a new human annotation file, it needs to be changed in run_param_config. changed back to the old code so it can pick up mouse annotation file. --- scripts/alignment_and_picard.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/scripts/alignment_and_picard.py b/scripts/alignment_and_picard.py index a188aca..d215878 100644 --- a/scripts/alignment_and_picard.py +++ b/scripts/alignment_and_picard.py @@ -258,8 +258,10 @@ def rna_alignment_and_metrics(sample, run, sample_parameters, rna_directory, wor metric_file = "{}___P{}___{}___{}".format(run, prjct, sample.sample_id, sample_parameters["GTAG"]) fastq_list = "/igo/staging/FASTQ/{}/Reports/fastq_list.csv ".format(run) - gtf_file = "/igo/work/genomes/H.sapiens/hg38/gencode.v40.chr_patch_hapl_scaff.annotation.gtf" - 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, gtf_file, metric_file, rna_directory) + # gtf_file = "/igo/work/genomes/H.sapiens/hg38/gencode.v40.chr_patch_hapl_scaff.annotation.gtf" + # having the gtf file hardcoded to human means that the mouse RNA samples will fail. + + 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"], metric_file, 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) print(bsub_launch_dragen_rna) call(bsub_launch_dragen_rna, shell = True)