add dual_mapping nf scripts

src/dual_mapping.config

+profiles {
+  sge {
+    process{
+      withName: index_fasta_hisat {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "hisat2/2.1.0:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        memory = "20GB"
+        cpus = 16
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: index_fasta_bowtie {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/bowtie_1.2.2"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        memory = "20GB"
+        cpus = 16
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: hisat2 {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "hisat2/2.1.0:samtools/1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        memory = "20GB"
+        cpus = 16
+        time = "12h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: sort_bam {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 1
+        memory = "20GB"
+        time = "12h"
+        queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
+      }
+      withName: merge_bam {
+        beforeScript = "source $baseDir/.conda_psmn.sh"
+        conda = "$baseDir/.conda_envs/samtools_1.7"
+        executor = "sge"
+        clusterOptions = "-cwd -V"
+        cpus = 16
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+    }
+  }
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta_hisat {
+        cpus = 4
+        container = "lbmc/hisat2:2.1.0"
+      }
+      withName: index_fasta_bowtie {
+        cpus = 4
+        container = "lbmc/bowtie:1.2.2"
+      }
+      withName: hisat2 {
+        cpus = 4
+        container = "lbmc/hisat2:2.1.0"
+      }
+      withName: bowtie {
+        cpus = 4
+        container = "lbmc/bowtie:1.2.2"
+      }
+      withName: merge_bam {
+        container = "lbmc/samtools:1.7"
+        cpus = 4
+      }
+    }
+  }
+}

src/dual_mapping.nf

+///////////////////////////////////////////////////////////////////////////////
+//////////////////////////////  INDEXING GENOMES  /////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
+params.fasta = "data/genome/NC001802.1.fa"
+log.info "fasta files : ${params.fasta}"
+
+Channel
+  .fromPath( params.fasta )
+  .ifEmpty { error "Cannot find any fasta files matching: ${params.fasta}" }
+  .set { fasta_file }
+
+fasta_file.into{fasta_hisat ; fasta_bowtie}
+
+/* HISAT */
+process index_fasta_hisat {
+  tag "$fasta.baseName"
+  publishDir "data/indexes/${fasta.baseName}_hisat/", mode: 'copy'
+
+  input:
+    file fasta from fasta_hisat
+
+  output:
+    file "*ht2" into index_files_hisat
+
+  script:
+"""
+hisat2-build -p ${task.cpus} ${fasta} ${fasta.baseName}
+"""
+}
+
+/* BOWTIE 1 */
+
+process index_fasta_bowtie {
+  tag "$fasta.baseName"
+  publishDir "results/${fasta.baseName}_bowtie/", mode: 'copy'
+
+  input:
+    file fasta from fasta_bowtie
+
+  output:
+    file "*ebwt" into index_files_bowtie
+    file "*_report.txt" into indexing_report
+
+  script:
+"""
+bowtie-build --threads ${task.cpus} -f ${fasta} ${fasta.baseName} \
+&> ${fasta.baseName}_bowtie_report.txt
+
+if grep -q "Error" ${fasta.baseName}_bowtie_report.txt; then
+  exit 1
+fi
+"""
+}
+
+///////////////////////////////////////////////////////////////////////////////
+//////////////////////////////  MAPPING GENOMES  /////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
+params.fastq = "$baseDir/data/fastq/*.fastq"
+// params.index = "$baseDir/data/index/*.index*"
+
+log.info "fastq files : ${params.fastq}"
+// log.info "index files : ${params.index}"
+
+Channel
+  .fromPath( params.fastq )
+  .ifEmpty { error "Cannot find any fastq files matching: ${params.fastq}" }
+  .map { it -> [(it.baseName =~ /([^\.]*)/)[0][1], it]}
+  .set { fastq_files }
+/*Channel
+  .fromPath( params.index )
+  .ifEmpty { error "Cannot find any index files matching: ${params.index}" }
+  .set { index_files }*/
+
+/* HISAIT */
+
+process hisat2 {
+  tag "$file_id"
+
+  input:
+    set file_id, file(fastq_filtred) from fastq_files
+    file index from index_files_hisat.collect()
+
+  output:
+    set file_id, "*.bam" into bam_hisat
+    file "*.txt" into hisat_report
+    set file_id, "*.fastq.gz" into reads_non_aligned
+
+  script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.ht2/ && !(index_file =~ /.*\.rev\.1\.ht2/)) {
+        index_id = ( index_file =~ /(.*)\.1\.ht2/)[0][1]
+    }
+  }
+"""
+hisat2 -x ${index_id} -p ${task.cpus} \
+-U ${fastq_filtred} --un-gz ${file_id}_notaligned_hisat.fastq.gz \
+--end-to-end --rna-strandness 'F' \
+2> ${file_id}_hisat2_NY5.txt | samtools view -F 4 -F 16 -Sb - > ${file_id}.bam
+"""
+}
+
+/* BOWTIE */
+
+process bowtie {
+  tag "$file_id"
+
+  input:
+  set file_id, file(reads) from reads_non_aligned
+  file index from index_files_bowtie.collect()
+
+  output:
+  set file_id, index_id, "*.bam" into bam_bowtie
+  file "*_report.txt" into mapping_report
+
+  script:
+index_id = index[0]
+for (index_file in index) {
+  if (index_file =~ /.*\.1\.ebwt/ && !(index_file =~ /.*\.rev\.1\.ebwt/)) {
+      index_id = ( index_file =~ /(.*)\.1\.ebwt/)[0][1]
+  }
+}
+"""
+bowtie --best --fr -v 3 -k 1 --sam -p ${task.cpus} ${index_id} \
+-q ${reads} 2> \
+${file_id}_bowtie_report_tmp.txt | \
+samtools view -F 4 -F 16 -Sb - > ${file_id}_bowtie.bam
+
+if grep -q "Error" ${file_id}_bowtie_report_tmp.txt; then
+  exit 1
+fi
+tail -n 19 ${file_id}_bowtie_report_tmp.txt > ${file_id}_bowtie_report.txt
+"""
+}
+
+///////////////////////////////////////////////////////////////////////////////
+//////////////////////////////  MERGE BAM  /////////////////////////////
+///////////////////////////////////////////////////////////////////////////////
+
+bam_bowtie.join(bam_hisat)
+          .set{merged_bam}
+
+//merged_bam.println()
+
+process merge_bam{
+  publishDir "results/05_${index_id}_mergedBAM/", mode: 'copy'
+
+  input:
+  set file_id, index_id, file(bam_bowtie), file(bam_hisat) from merged_bam
+
+  output:
+  file "*merged.{bam,bam.bai}" into final_flow
+
+  """
+  samtools sort -@ ${task.cpus} -o ${file_id}_bowtie_sort.bam ${bam_bowtie} && \
+  samtools sort -@ ${task.cpus} -o ${file_id}_hisat_sort.bam ${bam_hisat} && \
+  samtools merge ${file_id}_merged.bam *sort.bam && \
+  samtools index ${file_id}_merged.bam
+  """
+
+}