Merge pull request #31 from UMCUGenetics/feature/update_flask_tools

Update ExonCov commands
UMCUGenetics · Jun 11, 2024 · 9462d68 · 9462d68
2 parents 5ae3239 + f256cac
commit 9462d68
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diff --git a/ExonCov/ImportBam.nf b/ExonCov/ImportBam.nf
@@ -14,7 +14,7 @@ process ImportBam {
     script:
         """
         source ${params.exoncov_path}/venv/bin/activate
-        python ${params.exoncov_path}/ExonCov.py import_bam \
+        flask --app ${params.exoncov_path}/ExonCov import_bam \
         --threads ${task.cpus} \
         --overwrite \
         --print_sample_id \

diff --git a/ExonCov/SampleQC.nf b/ExonCov/SampleQC.nf
@@ -16,7 +16,7 @@ process SampleQC {
         def panels = indications.collect{"$it"}.join(" ")
         """
         source ${params.exoncov_path}/venv/bin/activate
-        python ${params.exoncov_path}/ExonCov.py sample_qc \
+        flask --app ${params.exoncov_path}/ExonCov sample_qc \
         -s ${samples} -p ${panels} > ${analysis_id}.ExonCovQC_check.out
         """
 }