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Gave names for localization tasks #16

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9e7ff31
Gave names for localization tasks
xaviloinaz Mar 5, 2024
93d3a48
catching silent error for convert_het_pulldown in workflow.py
xaviloinaz Jun 27, 2024
b889b09
catching silent error for convert_het_pulldown in workflow_interactiv…
xaviloinaz Jun 27, 2024
a44ef42
catching silent error for convert_het_pulldown in generate_raw_data.py
xaviloinaz Jun 27, 2024
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3 changes: 3 additions & 0 deletions benchmarking/generate_raw_data.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
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6 changes: 6 additions & 0 deletions wolF/workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,7 @@ def workflow(
# reference panel
**ref_config["ref_panel_1000g"]
),
name = "Localize_ref_files_HapASeg",
protect_disk = True
)

Expand All @@ -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
)
Expand All @@ -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
)
Expand Down Expand Up @@ -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",
Expand Down
3 changes: 3 additions & 0 deletions wolF/workflow_interactive.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down