Merge branch 'dev'

src/nf_modules/sambamba/index_bams.nf

+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+process index_bam {
+  tag "$file_id"
+  cpus 4
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*.bam*" into indexed_bam_file
+
+  script:
+"""
+sambamba index -t ${task.cpus} ${bam}
+"""
+}
+

src/nf_modules/sambamba/sort_bams.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $sort_bam {
+        container = "sambamba:0.6.7"
+      }
+    }
+  }
+  sge {
+    process{
+      $sort_bam {
+        beforeScript = "module purge; module load sambamba/0.6.7"
+      }
+    }
+  }
+}

src/nf_modules/sambamba/sort_bams.nf

+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+process sort_bam {
+  tag "$file_id"
+  cpus 4
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*_sorted.bam" into sorted_bam_files
+
+  script:
+"""
+sambamba sort -t ${task.cpus} -o ${file_id}_sorted.bam ${bam}
+"""
+}
+

src/nf_modules/sambamba/split_bams.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $split_bam {
+        container = "sambamba:0.6.7"
+      }
+    }
+  }
+  sge {
+    process{
+      $split_bam {
+        beforeScript = "module purge; module load sambamba/0.6.7"
+      }
+    }
+  }
+}

src/nf_modules/sambamba/split_bams.nf

+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { bam_files }
+
+process split_bam {
+  tag "$file_id"
+  cpus 4
+
+  input:
+    set file_id, file(bam) from bam_files
+
+  output:
+    set file_id, "*_forward.bam*" into forward_bam_files
+    set file_id, "*_reverse.bam*" into reverse_bam_files
+  script:
+"""
+sambamba view -t ${task.cpus} -h -F "strand == '+'" ${bam} > ${file_id}_forward.bam
+sambamba view -t ${task.cpus} -h -F "strand == '-'" ${bam} > ${file_id}_reverse.bam
+"""
+}
+

src/nf_modules/sambamba/tests.sh

+./nextflow src/nf_modules/sambamba/sort_bams.nf \
+  -c src/nf_modules/sambamba/sort_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam"
+
+./nextflow src/nf_modules/sambamba/index_bams.nf \
+  -c src/nf_modules/sambamba/index_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
+
+./nextflow src/nf_modules/sambamba/split_bams.nf \
+  -c src/nf_modules/sambamba/split_bams.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam"

src/nf_modules/samblaster/dedup_sams.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      $dedup_sam {
+        container = "samblaster:0.1.24"
+      }
+    }
+  }
+  sge {
+    process{
+      $dedup_sam {
+        beforeScript = "module purge; module load samblaster/0.1.24"
+      }
+    }
+  }
+}

src/nf_modules/samblaster/dedup_sams.nf

+params.sam = "$baseDir/data/sam/*.sam"
+
+log.info "sams files : ${params.sam}"
+
+Channel
+  .fromPath( params.sam )
+  .ifEmpty { error "Cannot find any sam files matching: ${params.sam}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { sam_files }
+
+process dedup_sam {
+  tag "$file_id"
+  cpus 4
+
+  input:
+    set file_id, file(sam) from sam_files
+
+  output:
+    set file_id, "*_dedup.sam*" into dedup_sam_files
+  script:
+"""
+samblaster --addMateTags -i ${sam} -o ${file_id}_dedup.sam
+"""
+}
+
+

src/nf_modules/samblaster/tests.sh

+./nextflow src/nf_modules/samblaster/dedup_sams.nf \
+  -c src/nf_modules/samblaster/dedup_sams.config \
+  -profile docker \
+  --sam "data/tiny_dataset/map/tiny_v2.sam"