even more threading

SFGLab · Jul 30, 2024 · a41e349 · a41e349
1 parent 8c3f12d
commit a41e349
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diff --git 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
@@ -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
@@ -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
     """
 }