threading & more memory

SFGLab · Jul 31, 2024 · 30a3846 · 30a3846
1 parent a41e349
commit 30a3846
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Showing 3 changed files with 13 additions and 13 deletions.
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/1.8.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 wget https://github.com/SFGLab/nf-hichip/archive/refs/tags/1.9.tar.gz && tar -xvzf 1.9.tar.gz && mv nf-hichip-1.9/* . && rm 1.9.tar.gz && rm -r nf-hichip-1.9
 
 RUN /opt/nextflow
diff --git a/main.nf b/main.nf
@@ -79,7 +79,7 @@ process Mapping {
 
     script:
     """
-    bwa mem -M -v 0 -t ${params.threads} ${params.ref} ${fastq1} ${fastq2} | samtools view -bh - > ${sample}_output.bam
+    bwa mem -M -v 0 -t ${params.threads} ${params.ref} ${fastq1} ${fastq2} | samtools view -@ ${params.threads} -bh - > ${sample}_output.bam
     """
 }
 
@@ -94,8 +94,8 @@ process FilterQuality {
 
     script:
     """
-    samtools view -F 0x04 -b ${mapped_bam} > ${sample}_output_removed_not_aligned.bam
-    samtools view -q ${params.mapq} -@ ${params.threads} -b ${sample}_output_removed_not_aligned.bam > ${sample}_output_filtered.bam
+    samtools view -@ ${params.threads} -F 0x04 -b ${mapped_bam} > ${sample}_output_removed_not_aligned.bam
+    samtools view -@ ${params.threads} -q ${params.mapq} -b ${sample}_output_removed_not_aligned.bam > ${sample}_output_filtered.bam
     """
 }
 
@@ -110,7 +110,7 @@ process RemoveDuplicates {
 
     script:
     """
-    samtools sort -n -@ ${params.threads} -m 1G ${bam} -o - | samtools fixmate -@ ${params.threads} - - | samtools rmdup -S - ${sample}_dedup.bam
+    samtools sort -n -@ ${params.threads} -m ${params.mem}G ${bam} -o - | samtools fixmate -@ ${params.threads} - - | samtools rmdup -S - ${sample}_dedup.bam
     """
 }
 

diff --git a/main_chipseq.nf b/main_chipseq.nf
@@ -86,8 +86,8 @@ process Mapping {
 
     script:
     """
-    bwa mem -M -v 0 -t ${params.threads} ${params.ref} ${fastq1} ${fastq2} | samtools view -bh - > ${sample}_output.bam
-    bwa mem -M -v 0 -t ${params.threads} ${params.ref} ${input1} ${input2} | samtools view -bh - > ${sample}_input_output.bam
+    bwa mem -M -v 0 -t ${params.threads} ${params.ref} ${fastq1} ${fastq2} | samtools view -@ ${params.threads} -bh - > ${sample}_output.bam
+    bwa mem -M -v 0 -t ${params.threads} ${params.ref} ${input1} ${input2} | samtools view -@ ${params.threads} -bh - > ${sample}_input_output.bam
     """
 }
 
@@ -104,10 +104,10 @@ process FilterQuality {
 
     script:
     """
-    samtools view -F 0x04 -b ${mapped_bam} > ${sample}_output_removed_not_aligned.bam
-    samtools view -F 0x04 -b ${bam_input} > ${sample}_input_output_removed_not_aligned.bam
-    samtools view -q ${params.mapq} -@ ${params.threads} -b ${sample}_output_removed_not_aligned.bam > ${sample}_output_filtered.bam
-    samtools view -q ${params.mapq} -@ ${params.threads} -b ${sample}_input_output_removed_not_aligned.bam > ${sample}_input_output_filtered.bam
+    samtools view -@ ${params.threads} -F 0x04 -b ${mapped_bam} > ${sample}_output_removed_not_aligned.bam
+    samtools view -@ ${params.threads} -F 0x04 -b ${bam_input} > ${sample}_input_output_removed_not_aligned.bam
+    samtools view -@ ${params.threads} -q ${params.mapq} -b ${sample}_output_removed_not_aligned.bam > ${sample}_output_filtered.bam
+    samtools view -@ ${params.threads} -q ${params.mapq} -b ${sample}_input_output_removed_not_aligned.bam > ${sample}_input_output_filtered.bam
     """
 }
 
@@ -124,8 +124,8 @@ process RemoveDuplicates {
 
     script:
     """
-    samtools sort -n -@ ${params.threads} -m 1G ${bam} -o - | samtools fixmate -@ ${params.threads} - - | samtools rmdup -S - ${sample}_dedup.bam
-    samtools sort -n -@ ${params.threads} -m 1G ${input_bam} -o - | samtools fixmate -@ ${params.threads} - - | samtools rmdup -S - ${sample}_input_dedup.bam
+    samtools sort -n -@ ${params.threads} -m ${params.mem}G ${bam} -o - | samtools fixmate -@ ${params.threads} - - | samtools rmdup -S - ${sample}_dedup.bam
+    samtools sort -n -@ ${params.threads} -m ${params.mem}G ${input_bam} -o - | samtools fixmate -@ ${params.threads} - - | samtools rmdup -S - ${sample}_input_dedup.bam
     """
 }