multithread samtools and bigwig

SFGLab · Jul 30, 2024 · 8c3f12d · 8c3f12d
1 parent 510b990
commit 8c3f12d
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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/1.6.tar.gz && tar -xvzf 1.6.tar.gz && mv nf-hichip-1.6/* . && rm 1.6.tar.gz && rm -r nf-hichip-1.6
+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 /opt/nextflow
diff --git a/main.nf b/main.nf
@@ -95,7 +95,7 @@ process FilterQuality {
     script:
     """
     samtools view -F 0x04 -b ${mapped_bam} > ${sample}_output_removed_not_aligned.bam
-    samtools view -q ${params.mapq} -t ${params.threads} -b ${sample}_output_removed_not_aligned.bam > ${sample}_output_filtered.bam
+    samtools view -q ${params.mapq} -@ ${params.threads} -b ${sample}_output_removed_not_aligned.bam > ${sample}_output_filtered.bam
     """
 }
 
@@ -110,7 +110,7 @@ process RemoveDuplicates {
 
     script:
     """
-    samtools sort -n -t ${params.threads} -m 1G ${bam} -o - | samtools fixmate --threads ${params.threads} - - | samtools rmdup -S - ${sample}_dedup.bam
+    samtools sort -n -@ ${params.threads} -m 1G ${bam} -o - | samtools fixmate -@ ${params.threads} - - | samtools rmdup -S - ${sample}_dedup.bam
     """
 }
 
@@ -126,9 +126,9 @@ process CreateBigwig {
 
     script:
     """
-    samtools sort -t ${params.threads} -m ${params.mem}G ${final_bam} -o ${sample}_output_final_sorted.bam
+    samtools sort -@ ${params.threads} -m ${params.mem}G ${final_bam} -o ${sample}_output_final_sorted.bam
     samtools index ${sample}_output_final_sorted.bam
-    bamCoverage -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig -p ${params.threads}
+    bamCoverage -p ${params.threads} -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig -p ${params.threads}
     """
 }
 

diff --git a/main_chipseq.nf b/main_chipseq.nf
@@ -106,8 +106,8 @@ process FilterQuality {
     """
     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} -t ${params.threads} -b ${sample}_output_removed_not_aligned.bam > ${sample}_output_filtered.bam
-    samtools view -q ${params.mapq} -t ${params.threads} -b ${sample}_input_output_removed_not_aligned.bam > ${sample}_input_output_filtered.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
     """
 }
 
@@ -124,8 +124,8 @@ process RemoveDuplicates {
 
     script:
     """
-    samtools sort -n -t ${params.threads} -m 1G ${bam} -o - | samtools fixmate --threads ${params.threads} - - | samtools rmdup -S - ${sample}_dedup.bam
-    samtools sort -n -t ${params.threads} -m 1G ${input_bam} -o - | samtools fixmate --threads ${params.threads} - - | samtools rmdup -S - ${sample}_input_dedup.bam
+    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
     """
 }
 
@@ -143,12 +143,12 @@ process CreateBigwig {
 
     script:
     """
-    samtools sort -t ${params.threads} -m ${params.mem}G ${final_bam} -o ${sample}_output_final_sorted.bam
+    samtools sort -@ ${params.threads} -m ${params.mem}G ${final_bam} -o ${sample}_output_final_sorted.bam
     samtools index ${sample}_output_final_sorted.bam
-    bamCoverage -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig -p ${params.threads}
-    samtools sort -t ${params.threads} -m ${params.mem}G ${input_final_bam} -o ${sample}_input_output_final_sorted.bam
+    bamCoverage -p ${params.threads} -b ${sample}_output_final_sorted.bam -o ${sample}_output.bigWig -p ${params.threads}
+    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 -b ${sample}_input_output_final_sorted.bam -o ${sample}_input_output.bigWig -p ${params.threads}
+    bamCoverage -p ${params.threads} -b ${sample}_input_output_final_sorted.bam -o ${sample}_input_output.bigWig -p ${params.threads}
     """
 }