SAMtools: add nf and test scripts

src/nf_modules/SAMtools/samtools.config

+profiles {
+  docker {
+    process {
+      $sort_bam {
+        container = "SAMtools:1.7"
+      }
+      $index_bam {
+        container = "SAMtools:1.7"
+      }
+      $split_bam {
+        container = "SAMtools:1.7"
+      }
+      $filter_bam {
+        container = "SAMtools:1.7"
+      }
+    }
+  }
+  sge {
+    process{
+      $trimming {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $index_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $split_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+      $filter_bam {
+        beforeScript = "module purge; module load SAMtools/1.7"
+      }
+    }
+  }
+}

src/nf_modules/SAMtools/samtools.nf

+/*
+* SAMtools :
+* Imputs : bam files
+* Output : bam files
+*/
+
+/*                      bams sorting                                     */
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .set { bam_files }
+
+process sort_bam {
+  tag "$bam.baseName"
+  cpus 4
+
+  input:
+    file bam from bam_files
+
+  output:
+    file "*_sorted.bam" into sorted_bam_files
+
+  script:
+"""
+samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
+"""
+}
+
+/*                      bams indexing                                     */
+
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .set { bam_files }
+
+process index_bam {
+  tag "$bam.baseName"
+  input:
+    file bam from bam_files
+  output:
+    file "*bam*" into indexed_bam_file
+  script:
+"""
+samtools index ${bam}
+"""
+}
+
+
+/*                      bams spliting                                     */
+params.bam = "$baseDir/data/bam/*.bam"
+
+log.info "bams files : ${params.bam}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .set { bam_files }
+
+process split_bam {
+  tag "$bam.baseName"
+  cpus 2
+
+  input:
+    file bam from bam_files
+
+  output:
+    file "*_forward.bam*" into forward_bam_files
+    file "*_reverse.bam*" into reverse_bam_files
+  script:
+"""
+samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
+samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
+"""
+}
+
+
+/*                      bams filtering                                     */
+params.bam = "$baseDir/data/bam/*.bam"
+params.bed = "$baseDir/data/bam/*.bed"
+
+log.info "bams files : ${params.bam}"
+log.info "bed file : ${params.bed}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .set { bam_files }
+Channel
+  .fromPath( params.bed )
+  .ifEmpty { error "Cannot find any bed file matching: ${params.bed}" }
+  .set { bed_files }
+
+process filter_bam {
+  tag "$bam.baseName"
+  cpus 4
+
+  input:
+    file bam from bam_files
+    file bed from bed_files
+
+  output:
+    file "*_filtered.bam*" into filtered_bam_files
+  script:
+"""
+samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${bam.baseName}_filtered.bam
+"""
+}
+
+

src/nf_modules/SAMtools/tests/filter_bams.nf

+params.bam = "$baseDir/data/bam/*.bam"
+params.bed = "$baseDir/data/bam/*.bed"
+
+log.info "bams files : ${params.bam}"
+log.info "bed file : ${params.bed}"
+
+Channel
+  .fromPath( params.bam )
+  .ifEmpty { error "Cannot find any bam files matching: ${params.bam}" }
+  .set { bam_files }
+Channel
+  .fromPath( params.bed )
+  .ifEmpty { error "Cannot find any bed file matching: ${params.bed}" }
+  .set { bed_files }
+
+process filter_bam {
+  tag "$bam.baseName"
+  cpus 4
+
+  input:
+    file bam from bam_files
+    file bed from bed_files
+
+  output:
+    file "*_filtered.bam*" into filtered_bam_files
+  script:
+"""
+samtools view -@ ${task.cpus} -hb ${bam} -L ${bed} > ${bam.baseName}_filtered.bam
+"""
+}
+
+

src/nf_modules/SAMtools/tests/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: ${params.bam}" }
+  .set { bam_files }
+
+process index_bam {
+  tag "$bam.baseName"
+  input:
+    file bam from bam_files
+  output:
+    file "*bam*" into indexed_bam_file
+  script:
+"""
+samtools index ${bam}
+"""
+}
+

src/nf_modules/SAMtools/tests/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: ${params.bam}" }
+  .set { bam_files }
+
+process sort_bam {
+  tag "$bams.baseName"
+  cpus 4
+
+  input:
+    file bam from bam_files
+
+  output:
+    file "*_sorted.bam" into sorted_bam_files
+
+  script:
+"""
+samtools sort -@ ${task.cpus} -O BAM -o ${bam.baseName}_sorted.bam ${bam}
+"""
+}
+

src/nf_modules/SAMtools/tests/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: ${params.bam}" }
+  .set { bam_files }
+
+process split_bam {
+  tag "$bam.baseName"
+  cpus 2
+
+  input:
+    file bam from bam_files
+
+  output:
+    file "*_forward.bam*" into forward_bam_files
+    file "*_reverse.bam*" into reverse_bam_files
+  script:
+"""
+samtools view -hb -F 0x10 ${bam} > ${bam}_forward.bam &
+samtools view -hb -f 0x10 ${bam} > ${bam}_reverse.bam
+"""
+}
+

src/nf_modules/SAMtools/tests/tests.sh

+nextflow src/nf_modules/SAMtools/tests/sort_bams.nf \
+  -c src/nf_modules/SAMtools/samtools.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam"
+
+nextflow src/nf_modules/SAMtools/tests/index_bams.nf \
+  -c src/nf_modules/SAMtools/samtools.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.sort.bam"
+
+nextflow src/nf_modules/SAMtools/tests/split_bams.nf \
+  -c src/nf_modules/SAMtools/samtools.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam"
+
+nextflow src/nf_modules/SAMtools/tests/filter_bams.nf \
+  -c src/nf_modules/SAMtools/samtools.config \
+  -profile docker \
+  --bam "data/tiny_dataset/map/tiny_v2.bam" \
+  --bed "data/tiny_dataset/OLD/2genes.bed"