From 9e7ff31ee2df9b613f01c90147a7ad247523f065 Mon Sep 17 00:00:00 2001 From: Xavi Loinaz Date: Tue, 5 Mar 2024 16:11:08 -0500 Subject: [PATCH 1/4] Gave names for localization tasks --- wolF/workflow.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wolF/workflow.py b/wolF/workflow.py index 834988b..d635508 100644 --- a/wolF/workflow.py +++ b/wolF/workflow.py @@ -201,6 +201,7 @@ def workflow( # reference panel **ref_config["ref_panel_1000g"] ), + name = "Localize_ref_files_HapASeg", protect_disk = True ) @@ -212,6 +213,7 @@ def workflow( "t_bam" : tumor_bam, "t_bai" : tumor_bai, }, + name = "Localize_T_bam_HapASeg", token=localization_token, persistent_disk_dry_run = persistent_dry_run ) @@ -229,6 +231,7 @@ def workflow( "n_bam" : normal_bam, "n_bai" : normal_bai }, + name = "Localize_N_bam_HapASeg", token=localization_token, persistent_disk_dry_run = persistent_dry_run ) From 93d3a48526b79bf70dedf16bd3acf1863fa3367f Mon Sep 17 00:00:00 2001 From: Xavi Loinaz Date: Thu, 27 Jun 2024 17:45:54 -0400 Subject: [PATCH 2/4] catching silent error for convert_het_pulldown in workflow.py --- wolF/workflow.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wolF/workflow.py b/wolF/workflow.py index d635508..e03c01b 100644 --- a/wolF/workflow.py +++ b/wolF/workflow.py @@ -469,6 +469,9 @@ def interval_gather(interval_files, primary_contigs): for chr in $(bcftools view -h all_chrs.bcf | ssed -nR '/^##contig/s/.*ID=(.*),.*/\1/p' | head -n24); do bcftools view -Ou -r ${chr} -o ${chr}.chrsplit.bcf all_chrs.bcf && bcftools index ${chr}.chrsplit.bcf done + if ! ls *.chrsplit.bcf 1> /dev/null 2>&1; then + exit 1 # This is to account for when silent errors are thrown where convert_het_pulldown does not write its output properly and throws an error but wolF does not catch this + fi """, outputs = { "bcf" : "*.chrsplit.bcf", From b889b0983d48a9c162b531cf447680776a527fbb Mon Sep 17 00:00:00 2001 From: Xavi Loinaz Date: Thu, 27 Jun 2024 17:46:50 -0400 Subject: [PATCH 3/4] catching silent error for convert_het_pulldown in workflow_interactive.py --- wolF/workflow_interactive.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/wolF/workflow_interactive.py b/wolF/workflow_interactive.py index 9f06a05..554abef 100644 --- a/wolF/workflow_interactive.py +++ b/wolF/workflow_interactive.py @@ -84,6 +84,9 @@ for chr in $(bcftools view -h all_chrs.bcf | ssed -nR '/^##contig/s/.*ID=(.*),.*/\1/p' | head -n24); do bcftools view -Ou -r ${chr} -o ${chr}.chrsplit.bcf all_chrs.bcf && bcftools index ${chr}.chrsplit.bcf done +if ! ls *.chrsplit.bcf 1> /dev/null 2>&1; then + exit 1 # This is to account for when silent errors are thrown where convert_het_pulldown does not write its output properly and throws an error but wolF does not catch this +fi """, outputs = { "bcf" : "*.chrsplit.bcf", From a44ef4201c23e4af8bb2b6a9c5b92015e4010cfc Mon Sep 17 00:00:00 2001 From: Xavi Loinaz Date: Thu, 27 Jun 2024 17:48:18 -0400 Subject: [PATCH 4/4] catching silent error for convert_het_pulldown in generate_raw_data.py --- benchmarking/generate_raw_data.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/benchmarking/generate_raw_data.py b/benchmarking/generate_raw_data.py index 7365067..a687620 100644 --- a/benchmarking/generate_raw_data.py +++ b/benchmarking/generate_raw_data.py @@ -293,6 +293,9 @@ def interval_gather(interval_files, primary_contigs): for chr in $(bcftools view -h all_chrs.bcf | ssed -nR '/^##contig/s/.*ID=(.*),.*/\1/p' | head -n24); do bcftools view -Ou -r ${chr} -o ${chr}.chrsplit.bcf all_chrs.bcf && bcftools index ${chr}.chrsplit.bcf done + if ! ls *.chrsplit.bcf 1> /dev/null 2>&1; then + exit 1 # This is to account for when silent errors are thrown where convert_het_pulldown does not write its output properly and throws an error but wolF does not catch this + fi """, outputs = { "bcf" : "*.chrsplit.bcf",