From 3c334deb68edcd4a0e983d7918538915a405661f Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 23 May 2024 11:08:58 +0200
Subject: [PATCH 1/2] Update ExonCov commands

---
 ExonCov/ImportBam.nf | 2 +-
 ExonCov/SampleQC.nf  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ExonCov/ImportBam.nf b/ExonCov/ImportBam.nf
index 474ae35..4deaa58 100644
--- 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 ExonCov import_bam \
         --threads ${task.cpus} \
         --overwrite \
         --print_sample_id \
diff --git a/ExonCov/SampleQC.nf b/ExonCov/SampleQC.nf
index 49ecf2d..e381ce3 100644
--- a/ExonCov/SampleQC.nf
+++ b/ExonCov/SampleQC.nf
@@ -16,7 +16,7 @@ process SampleQC {
         def panels = indications.collect{"$it"}.join(" ")
         """
         source ${params.exoncov_path}/venv/bin/activate
-        python ${params.exoncov_path}/ExonCov.py sample_qc \
+        flask --app ExonCov sample_qc \
         -s ${samples} -p ${panels} > ${analysis_id}.ExonCovQC_check.out
         """
 }
\ No newline at end of file

From f256cacee72a63bdd4c6592dd5cf4f80984c25bb Mon Sep 17 00:00:00 2001
From: Robert Ernst <r.f.ernst-3@umcutrecht.nl>
Date: Thu, 23 May 2024 11:28:30 +0200
Subject: [PATCH 2/2] Revert exoncov_path

---
 ExonCov/ImportBam.nf | 2 +-
 ExonCov/SampleQC.nf  | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/ExonCov/ImportBam.nf b/ExonCov/ImportBam.nf
index 4deaa58..6afbfe8 100644
--- a/ExonCov/ImportBam.nf
+++ b/ExonCov/ImportBam.nf
@@ -14,7 +14,7 @@ process ImportBam {
     script:
         """
         source ${params.exoncov_path}/venv/bin/activate
-        flask --app ExonCov import_bam \
+        flask --app ${params.exoncov_path}/ExonCov import_bam \
         --threads ${task.cpus} \
         --overwrite \
         --print_sample_id \
diff --git a/ExonCov/SampleQC.nf b/ExonCov/SampleQC.nf
index e381ce3..a297325 100644
--- a/ExonCov/SampleQC.nf
+++ b/ExonCov/SampleQC.nf
@@ -16,7 +16,7 @@ process SampleQC {
         def panels = indications.collect{"$it"}.join(" ")
         """
         source ${params.exoncov_path}/venv/bin/activate
-        flask --app ExonCov sample_qc \
+        flask --app ${params.exoncov_path}/ExonCov sample_qc \
         -s ${samples} -p ${panels} > ${analysis_id}.ExonCovQC_check.out
         """
 }
\ No newline at end of file