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fix: use conda only in cadd scripts #18

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Merged
merged 1 commit into from
Dec 3, 2024
Merged

fix: use conda only in cadd scripts #18

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6 changes: 3 additions & 3 deletions helpers/CADD_mocker.sh
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
#!/bin/bash

cat << "EOF" > "$7"
cat << "EOF" > "$8"
#Chrom Pos Ref Alt RawScore PHRED
1 100 A G 0.1 0.1
1 200 C T 0.2 0.2
EOF

gzip -c "$7" > "$7.tmp"
mv "$7.tmp" "$7"
gzip -c "$8" > "$8.tmp"
mv "$8.tmp" "$8"
2 changes: 1 addition & 1 deletion restapi/tasks.py
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ def annotate_background_job(_self, bgjob_uuid):
"bash",
"-xc",
(
"{conda_activate}{cadd_sh} -a -g {genome_build} -v {cadd_release} "
"{conda_activate}{cadd_sh} -m -a -g {genome_build} -v {cadd_release} "
"-o {tmpdir}/out.tsv.gz {tmpdir}/in.vcf"
).format(
conda_activate=("source %s; " % CADD_CONDA) if CADD_CONDA else "",
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