From c1e6690a39a88e614cdb3d8a4abe61df810d667d Mon Sep 17 00:00:00 2001
From: pd321 <52960055+pd321@users.noreply.github.com>
Date: Sun, 26 Apr 2020 16:51:24 +0530
Subject: [PATCH] Fixes #4 and #5

---
 src/align.smk | 19 ++++++++++++-------
 src/se.smk    |  2 +-
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/align.smk b/src/align.smk
index 0b0b133..09ecfa9 100644
--- a/src/align.smk
+++ b/src/align.smk
@@ -6,9 +6,11 @@ rule trimgalore_se:
 	params:
 		quality = config['trimgalore']['quality'],
 		stringency = config['trimgalore']['stringency'],
-		e = config['trimgalore']['e']
-	# trimgalore does not recommend using more than 4 threads
-	threads: threads_mid if threads_mid < 4 else 4
+		e = config['trimgalore']['e'],
+		#trimgalore does not recommend using more than 4 threads
+		threads_actual = threads_mid if threads_mid < 4 else 4
+	# setting it to mid ensures not no many trimgalore jobs launched
+	threads: threads_mid
 	shell:
 		'trim_galore '
 		'--quality {params.quality} '
@@ -16,7 +18,7 @@ rule trimgalore_se:
 		'-e {params.e} '
 		'--gzip '
 		'--output_dir results/bam/ '
-		'--cores {threads} '
+		'--cores {params.threads_actual} '
 		'--basename {wildcards.sample} '
 		'--no_report_file '
 		'{input} 2>&1 | tee {log}'
@@ -34,8 +36,11 @@ rule trimgalore_pe:
 	params:
 		quality = config['trimgalore']['quality'],
 		stringency = config['trimgalore']['stringency'],
-		e = config['trimgalore']['e']
-	threads: threads_mid if threads_mid < 4 else 4
+		e = config['trimgalore']['e'],
+		#trimgalore does not recommend using more than 4 threads
+		threads_actual = threads_mid if threads_mid < 4 else 4
+	# setting it to mid ensures not no many trimgalore jobs launched
+	threads: threads_mid
 	shell:
 		'trim_galore '
 		'--quality {params.quality} '
@@ -43,7 +48,7 @@ rule trimgalore_pe:
 		'-e {params.e} '
 		'--gzip '
 		'--output_dir results/bam/ '
-		'--cores 4 '
+		'--cores {params.threads_actual} '
 		'--basename {wildcards.sample} '
 		'--paired --no_report_file '
 		'{input[0]} {input[1]} 2>&1 | tee {log}'
diff --git a/src/se.smk b/src/se.smk
index ce8fccd..70481b3 100644
--- a/src/se.smk
+++ b/src/se.smk
@@ -5,7 +5,7 @@ rule rose_main:
 		peaks = rules.blklist_filt.output
 	output:
 		enhancers_table = "results/se/{chip_sample}/{chip_sample}_peaks_AllEnhancers.table.txt",
-		enhancers_plot = "results/se/{chip_sample}/{chip_sample}_Plot_points.png"
+		enhancers_plot = "results/se/{chip_sample}/{chip_sample}_peaks_Plot_points.png"
 	threads: threads_mid
 	log: "logs/se/{chip_sample}_rose_main.log"
 	params: