macs3: add main.nf

src/nf_modules/macs3/main.nf

+version = "3.0.0a6"
+container_url = "lbmc/macs3:${version}"
+
+process peak_calling {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "${file_id}"
+
+  input:
+    tuple val(file_id), path(bam_ip), path(bam_control)
+
+  output:
+    path "*", emit: peak
+    path "*_report.txt", emit: report
+
+  script:
+/* remove --nomodel option for real dataset */
+"""
+macs2 callpeak \
+  --treatment ${file_ip} \
+  --call-summits "True"\
+  --control ${file_control} \
+  --keep-dup "auto" \
+  --name ${bam_ip.simpleName} \
+  --gsize ${macs3_genome_size} 2> \
+  ${bam_ip.simpleName}_macs3_report.txt
+
+if grep -q "ERROR" ${bam_ip.simpleName}_macs3_report.txt; then
+  echo "MACS3 error"
+  exit 1
+fi
+"""
+}
+
+process peak_calling_bg {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+  tag "${file_id}"
+
+  input:
+    tuple val(file_id), path(bg_ip), path(bg_control)
+
+  output:
+    path "*", emit: peak
+    path "*_report.txt", emit: report
+
+  script:
+/* remove --nomodel option for real dataset */
+"""
+awk '{print $1"\t"$2"\t"$3"\t.\t+\t"$4}' ${file_ip} > \
+  ${file_ip.simpleName}.bed
+awk '{print $1"\t"$2"\t"$3"\t.\t+\t"$4}' ${file_control} > \
+  ${file_control.simpleName}.bed
+macs2 callpeak \
+  --treatment ${file_ip.simpleName}.bed \
+  --call-summits "True"\
+  --control ${file_control.simpleName}.bed \
+  --keep-dup "auto" \
+  --name ${bam_ip.simpleName} \
+  --gsize ${macs3_genome_size} 2> \
+  ${bam_ip.simpleName}_macs3_report.txt
+
+if grep -q "ERROR" ${bam_ip.simpleName}_macs3_report.txt; then
+  echo "MACS3 error"
+  exit 1
+fi
+"""
+}
+