From 5ca30c98201d6d82ffb6e43d976ff4a4fab0bdf3 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sat, 29 Feb 2020 09:08:27 -0600
Subject: [PATCH] Update for bats testing.
---
workflow/main.nf | 2 +-
workflow/scripts/plot_profile.sh | 87 +++++++++++++++++++++++++++-----
workflow/tests/plot_profile.bats | 19 +++++++
3 files changed, 94 insertions(+), 14 deletions(-)
mode change 100644 => 100755 workflow/scripts/plot_profile.sh
create mode 100644 workflow/tests/plot_profile.bats
diff --git a/workflow/main.nf b/workflow/main.nf
index 045afd4..cb8b1e6 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -496,7 +496,7 @@ process plotProfile {
script:
"""
module load deeptools/2.5.0.1
- bash $baseDir/scripts/plot_profile.sh $gtfFile
+ bash $baseDir/scripts/plot_profile.sh
"""
}
diff --git a/workflow/scripts/plot_profile.sh b/workflow/scripts/plot_profile.sh
old mode 100644
new mode 100755
index b4df3b3..09b15eb
--- a/workflow/scripts/plot_profile.sh
+++ b/workflow/scripts/plot_profile.sh
@@ -1,16 +1,77 @@
#!/bin/bash
#plot_profile.sh
-bws=$(ls *.bw)
-gtf=$(ls *.gtf *.bed)
-
-computeMatrix reference-point \
- --referencePoint TSS \
- -S $bws \
- -R $gtf \
- --skipZeros \
- -o computeMatrix.gz
- -p max/2
-
-plotProfile -m computeMatrix.gz \
- -out plotProfile.png \
+raise()
+{
+ echo "${1}" >&2
+}
+
+check_tools() {
+ raise "
+ Checking for required libraries and components on this system
+ "
+ deeptools --version &> version_deeptools.txt
+ if [ $? -gt 0 ]
+ then
+ raise "Missing deeptools"
+ return 1
+ fi
+}
+
+compute_matrix() {
+ raise "
+ Computing matrix on ${1} using ${2}
+ "
+
+ computeMatrix reference-point \
+ --referencePoint TSS \
+ -S ${1} \
+ -R ${2} \
+ --skipZeros \
+ -o computeMatrix.gz \
+ -p max/2
+
+ if [ $? -gt 0 ]
+ then
+ raise "Problem building matrix"
+ return 1
+ fi
+}
+
+plot_profile() {
+ raise "
+ Plotting profile
+ "
+
+ plotProfile -m computeMatrix.gz \
+ -out plotProfile.png
+
+ if [ $? -gt 0 ]
+ then
+ raise "Problem plotting"
+ return 1
+ fi
+}
+
+
+run_main() {
+ bws=$(ls *.bw)
+ gtf=$(ls *.gtf *.bed)
+
+ check_tools || exit 1
+
+ compute_matrix "${bws}" "${gtf}" || return 1
+
+ plot_profile || return 1
+
+ raise "ALL COMPLETE"
+}
+
+if [[ "${BASH_SOURCE[0]}" == "${0}" ]]
+then
+ run_main
+ if [ $? -gt 0 ]
+ then
+ exit 1
+ fi
+fi
diff --git a/workflow/tests/plot_profile.bats b/workflow/tests/plot_profile.bats
new file mode 100644
index 0000000..63fd7dd
--- /dev/null
+++ b/workflow/tests/plot_profile.bats
@@ -0,0 +1,19 @@
+#!/opt/bats/libexec/bats-core/ bats
+
+profile_script="./worflow/scripts/plot_profile.sh"
+
+setup() {
+ module load deeptools/2.5.0.1
+}
+
+@test "Test deeptools present" {
+ source ${profile_script}
+ run check_tools
+ assert_success
+}
+
+@test "Test matrix generation" {
+ source ${profile_script}
+ run check_tools
+ assert_success
+}
--
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