From 91fd6c15ff84010655a395f3f3a219fb258d1b29 Mon Sep 17 00:00:00 2001
From: Ally Hawkins <ally.hawkins@ccdatalab.org>
Date: Thu, 2 Jun 2022 21:35:27 -0500
Subject: [PATCH] add command line arguments for DTU pipeline

---
 splice_pipeline.sh | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/splice_pipeline.sh b/splice_pipeline.sh
index 948a3da..73f3b8d 100644
--- a/splice_pipeline.sh
+++ b/splice_pipeline.sh
@@ -446,12 +446,13 @@ junc_calling=($(sbatch --dependency=singleton --job-name="$sample_name" "$script
 ## step 6: Differential transcript usage (with permutations within cell types)
 
 diff_transcript=($(sbatch --dependency=singleton --job-name="$sample_name" "$scripts_dir"/diff_transcript_usage/diff_transcript_pipeline.sh \
-  "$output_dir"/output_files \
-  $run_files \
-  "$output_dir"/output_files/leafcutter_outputs/"$sample_name"_output/"$sample_name"_all.introns.info.w.primary.annotations.txt \
-  "$output_dir"/output_files/leafcutter_outputs/"$sample_name"_output/"$sample_name"_perind_numbers.counts.txt  \
-  $genotype_info \
-  $pattern \
-  $sample_name \
-  $nperm))
+  --output_dir "$output_dir"/output_files \
+  --scripts_dir $scripts_dir/diff_transcript_usage \
+  --metadata "$output_dir"/output_files/leafcutter_outputs/"$sample_name"_output/"$sample_name"_all.introns.info.w.primary.annotations.txt \
+  --counts "$output_dir"/output_files/leafcutter_outputs/"$sample_name"_output/"$sample_name"_perind_numbers.counts.txt  \
+  --genotype_info $genotype_info \
+  --pattern $pattern \
+  --sample_name $sample_name \
+  --nperm $nperm \
+  --min_reads $min_reads))
 '