MUSIC: nf files for single-end data

src/nf_modules/MUSIC/peak_calling_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $compute_mappability {
+        container = "music:6613c53"
+      }
+      $music_preprocessing {
+        container = "music:6613c53"
+      }
+      $music_sort {
+        container = "music:6613c53"
+      }
+      $music_dedup {
+        container = "music:6613c53"
+      }
+      $music_computation {
+        container = "music:6613c53"
+      }
+    }
+  }
+  sge {
+    process{
+      $compute_mappability {
+        beforeScript = "module purge; module load MUSIC/6613c53"
+      }
+      $music_preprocessing {
+        beforeScript = "module purge; module load MUSIC/6613c53"
+      }
+      $music_sort {
+        beforeScript = "module purge; module load MUSIC/6613c53"
+      }
+      $music_dedup {
+        beforeScript = "module purge; module load MUSIC/6613c53"
+      }
+      $music_computation {
+        beforeScript = "module purge; module load MUSIC/6613c53"
+      }
+    }
+  }
+}

src/nf_modules/MUSIC/peak_calling_single.nf

+params.reads_size = 100
+params.frag_size = 200
+params.begin_l = 50
+params.end_l = 500
+
+log.info "bam files : ${params.bam}"
+log.info "index files : ${params.index}"
+log.info "fasta files : ${params.fasta}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.fasta}" }
+  .set { fasta_files }
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }
+
+process compute_mappability {
+  tag "${fasta.baseName}"
+
+  input:
+    file index from index_files.collect()
+    file fasta from fasta_files
+
+  output:
+    file "*.bin" into mappability
+    file "temp/chr_ids.txt" into chr_ids
+
+  script:
+
+"""
+generate_multimappability_signal.csh ${fasta} ${params.reads_size} ./
+bash temp_map_reads.csh
+bash temp_process_mapping.csh
+"""
+}
+
+process music_preprocessing {
+  tag "${file_id}"
+
+  input:
+    set file_id, file(bam) from bam_files
+    file chr_ids from chr_ids.collect()
+
+  output:
+    set file_id, "preprocessed/*.tar" into preprocessed_bam_files
+
+  script:
+
+"""
+mkdir preprocessed
+samtools view *.bam | \
+MUSIC -preprocess SAM stdin preprocessed/
+mkdir preprocessed/sorted
+MUSIC -sort_reads preprocessed/ preprocessed/sorted/
+mkdir preprocessed/dedup
+MUSIC -remove_duplicates ./preprocessed/sorted 2 preprocessed/dedup/
+cd preprocessed
+tar -c -f ${file_id}.tar *
+"""
+}
+
+preprocessed_bam_files_control = Channel.create()
+preprocessed_bam_files_chip = Channel.create()
+preprocessed_bam_files.choice(
+  preprocessed_bam_files_control,
+  preprocessed_bam_files_chip ) { a -> a[0] =~ /.*control.*/ ? 0 : 1 }
+
+process music_computation {
+  tag "${file_id}"
+  publishDir "results/peak_calling/${file_id}", mode: 'copy'
+
+  input:
+    set file_id, file(control) from preprocessed_bam_files_chip
+    set file_id_control, file(chip) from preprocessed_bam_files_control.collect()
+    file mapp from mappability.collect()
+
+  output:
+    file "*" into music_output_forward
+    file "*.bed" into peaks_forward
+
+  script:
+
+"""
+mkdir mappability control chip
+mv ${mapp} mappability/
+tar -xf ${control} -C control/
+tar -xf ${chip} -C chip/
+
+MUSIC -get_per_win_p_vals_vs_FC -chip chip/ -control control/ \
+  -l_win_step ${params.end_l} \
+  -l_win_min ${params.end_l} -l_win_max ${params.end_l * 10}
+MUSIC -get_multiscale_punctate_ERs \
+  -chip chip/ -control control/ -mapp mappability/ \
+  -begin_l ${params.begin_l} -end_l ${params.end_l} -step 1.1 \
+  -l_mapp ${params.reads_size} -l_frag ${params.frag_size} -q_val 1 -l_p 0
+ls -l
+"""
+}