From 1b95ade8cd3100f8342a2f659902201009c955a1 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 19 Jun 2018 13:59:49 -0500
Subject: [PATCH] Fix check design file.
---
workflow/main.nf | 2 +-
workflow/scripts/check_design.py | 4 +++-
2 files changed, 4 insertions(+), 2 deletions(-)
diff --git a/workflow/main.nf b/workflow/main.nf
index 1d1d6af..2736346 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -61,7 +61,7 @@ process checkDesignFile {
}
else {
"""
- python $baseDir/scripts/check_design.py -d $designFile -f $readsList -a
+ python3 $baseDir/scripts/check_design.py -d $designFile -f $readsList -a
"""
}
diff --git a/workflow/scripts/check_design.py b/workflow/scripts/check_design.py
index 3822e74..e83c9c6 100644
--- a/workflow/scripts/check_design.py
+++ b/workflow/scripts/check_design.py
@@ -158,9 +158,11 @@ def main():
fastq_df = pd.read_csv(fastq, sep='\t', names=['name', 'path'])
# Check design file
- check_design_headers(design_df, paired)
+ check_design_headers(design_df, paired, atac)
+
if not atac:
check_controls(design_df)
+
check_replicates(design_df)
new_design_df = check_files(design_df, fastq_df, paired)
--
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