:mapping

src/RNASeq.config

@@ -12,6 +12,13 @@ profiles {
       withName: fasta_from_bed {
         container = "bedtools:2.25.0"
       }
+      withName: index_fasta {
+        container = "kallisto:0.44.0"
+      }
+      withName: mapping_fastq {
+        container = "kallisto:0.44.0"
+      }
+
     }
   }
   psmn {
@@ -44,6 +51,26 @@ profiles {
         time = "12h"
         queue = 'monointeldeb128'
       }
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Kallisto/0.44.0"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "Kallisto/0.44.0"
+        executor = "sge"
+        clusterOptions = "-m e -cwd -V"
+        memory = "30GB"
+        time = "24h"
+        queue = 'E5-2670deb128A,E5-2670deb128B,E5-2670deb128C,E5-2670deb128D,E5-2670deb128E,E5-2670deb128F'
+        penv = 'openmp16'
+      }
     }
   }
 }                                                                                              .

src/RNASeq.nf

@@ -88,3 +88,45 @@ bedtools getfasta -name \
 }
 
 
+process index_fasta {
+  tag "$fasta.baseName"
+  cpus 4
+  publishDir "results/mapping/index/", mode: 'copy'
+
+  input:
+    file fasta from fasta_file_extracted
+
+  output:
+    file "*.index*" into index_files
+    file "*_kallisto_report.txt" into index_files_report
+
+  script:
+"""
+kallisto index -k 31 --make-unique -i ${fasta.baseName}.index ${fasta} \
+2> ${fasta.baseName}_kallisto_report.txt
+"""
+}
+
+process mapping_fastq {
+  tag "$reads"
+  cpus 4
+  publishDir "results/mapping/quantification/", mode: 'copy'
+
+  input:
+  set pair_id, file(reads) from fastq_files_trim
+  file index from index_files.collect()
+
+  output:
+  file "*" into counts_files
+
+  script:
+"""
+mkdir ${pair_id}
+kallisto quant -i ${index} -t ${task.cpus} \
+--bias --bootstrap-samples 100 -o ${pair_id} \
+${reads[0]} ${reads[1]} &> ${pair_id}/kallisto_report.txt
+"""
+}
+
+
+