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", diff --git a/wolF/workflow.py b/wolF/workflow.py index 834988b..e03c01b 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 ) @@ -466,6 +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", 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",