From 4a5c7507595049ff65c21e38b5102598efa77f4f Mon Sep 17 00:00:00 2001 From: darrelln32 Date: Sun, 3 Sep 2023 20:09:49 -0400 Subject: [PATCH] Update LaunchMetrics.py change script to use hash tables on igo cluster since i have limited availability to internet access --- scripts/LaunchMetrics.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/scripts/LaunchMetrics.py b/scripts/LaunchMetrics.py index b2e3ebd..5f8238b 100644 --- a/scripts/LaunchMetrics.py +++ b/scripts/LaunchMetrics.py @@ -123,9 +123,9 @@ def rna_alignment_and_metrics(sample, run, sample_parameters, rna_directory, wor # get the correct path for the reference if (sample_parameters["GTAG"] == "GRCh38"): - rna_path = "/staging/ref/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559" + rna_path = "/igo/work/igo/dragen_hash_tables/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559" else: - rna_path = "/staging/ref/{}".format(sample_parameters["GTAG"]) + rna_path = "/igo/work/igo/dragen_hash_tables/{}".format(sample_parameters["GTAG"]) rna_dragen_job_name_header = "{}___RNA_DRAGEN___".format(run) @@ -160,9 +160,9 @@ def dragen(sample, run, sample_parameters, work_directory, dragen_directory, fas # get the correct path for the reference if (sample_parameters["GTAG"] == "GRCh38"): - dragen_path = "/staging/ref/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559" + dragen_path = "/igo/work/igo/dragen_hash_tables/hg38_alt_masked_graph_v2+cnv+graph+rna-8-1644018559" else: - dragen_path = "/staging/ref/{}".format(sample_parameters["GTAG"]) + dragen_path = "/igo/work/igo/dragen_hash_tables/{}".format(sample_parameters["GTAG"]) 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) @@ -203,9 +203,9 @@ def dragen_methylation(sample, run, sample_parameters, work_directory, dragen_di # get the correct path for the reference if (sample_parameters["GTAG"] == "GRCh38"): - dragen_path = "/staging/ref/hg38_methylated" + dragen_path = "/igo/work/igo/dragen_hash_tables/hg38_methylated" else: - dragen_path = "/staging/ref/grcm39_methylated" + dragen_path = "/igo/work/igo/dragen_hash_tables/grcm39_methylated" 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)