From a41e3490c30e8812917643d09b6646107d66b76a Mon Sep 17 00:00:00 2001
From: Mateusz Chilinski <mateusz@chilinski.eu>
Date: Tue, 30 Jul 2024 12:39:36 +0200
Subject: [PATCH] even more threading

---
 Dockerfile      | 2 +-
 main.nf         | 4 ++--
 main_chipseq.nf | 8 ++++----
 3 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 81592de..64327d4 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -81,6 +81,6 @@ RUN pip3 install plumbum
 
 RUN curl -s https://get.nextflow.io | bash && mv nextflow /opt/
 
-RUN wget https://github.com/SFGLab/nf-hichip/archive/refs/tags/1.7.tar.gz && tar -xvzf 1.7.tar.gz && mv nf-hichip-1.7/* . && rm 1.7.tar.gz && rm -r nf-hichip-1.7
+RUN wget https://github.com/SFGLab/nf-hichip/archive/refs/tags/1.8.tar.gz && tar -xvzf 1.8.tar.gz && mv nf-hichip-1.8/* . && rm 1.8.tar.gz && rm -r nf-hichip-1.8
 
 RUN /opt/nextflow
diff --git a/main.nf b/main.nf
index 37ab7ff..28c9b4a 100644
--- a/main.nf
+++ b/main.nf
@@ -127,8 +127,8 @@ process CreateBigwig {
     script:
     """
     samtools sort -@ ${params.threads} -m ${params.mem}G ${final_bam} -o ${sample}_output_final_sorted.bam
-    samtools index ${sample}_output_final_sorted.bam
-    bamCoverage -p ${params.threads} -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig -p ${params.threads}
+    samtools index -@ ${params.threads} ${sample}_output_final_sorted.bam
+    bamCoverage -p ${params.threads} -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig
     """
 }
 
diff --git a/main_chipseq.nf b/main_chipseq.nf
index 70df770..aff0c5e 100644
--- a/main_chipseq.nf
+++ b/main_chipseq.nf
@@ -144,11 +144,11 @@ process CreateBigwig {
     script:
     """
     samtools sort -@ ${params.threads} -m ${params.mem}G ${final_bam} -o ${sample}_output_final_sorted.bam
-    samtools index ${sample}_output_final_sorted.bam
-    bamCoverage -p ${params.threads} -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig -p ${params.threads}
+    samtools index -@ ${params.threads} ${sample}_output_final_sorted.bam
+    bamCoverage -p ${params.threads} -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig
     samtools sort -@ ${params.threads} -m ${params.mem}G ${input_final_bam} -o ${sample}_input_output_final_sorted.bam
-    samtools index ${sample}_input_output_final_sorted.bam
-    bamCoverage -p ${params.threads} -b ${sample}_input_output_final_sorted.bam -o ${sample}_input_output.bigWig -p ${params.threads}
+    samtools index -@ ${params.threads} ${sample}_input_output_final_sorted.bam
+    bamCoverage -p ${params.threads} -b ${sample}_input_output_final_sorted.bam -o ${sample}_input_output.bigWig
     """
 }