hisat2: update process and config to match new format

src/nf_modules/hisat2/indexing.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: index_fasta {
+        cpus = 4
+        container = "hisat2:2.0.0"
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: index_fasta {
+        cpus = 4
+        container = "file://bin/hisat2:2.0.0.sif"
+      }
+    }
+  }
+  sge {
+    process{
+      withName: index_fasta {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "hisat2/2.0.0"
+        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'
+      }
+    }
+  }
+}

src/nf_modules/hisat2/test/index.nf → src/nf_modules/hisat2/indexing.nf

@@ -27,6 +27,6 @@ process index_fasta {
 
   script:
 """
-hisat2-build ${fasta} ${fasta.baseName}.index
+hisat2-build -p {task.cpus} ${fasta} ${fasta.baseName}.index
 """
 }

src/nf_modules/hisat2/mapping_paired.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        cpus = 4
+        container = "hisat2:2.0.0"
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        cpus = 4
+        container = "file://bin/hisat2:2.0.0.sif"
+      }
+    }
+  }
+  sge {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "hisat2/2.0.0"
+        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'
+      }
+    }
+  }
+}

src/nf_modules/hisat2/test/mapping_paired.nf → src/nf_modules/hisat2/mapping_paired.nf

@@ -14,20 +14,24 @@ Channel
   .set { index_files }
 
 process mapping_fastq {
-  tag "$reads"
-  //tag "$index.baseName"
-  cpus 4
+  tag "$pair_id"
   publishDir "results/mapping/", mode: 'copy'
 
   input:
   set pair_id, file(reads) from fastq_files
-  file index from index_files.toList()
+  file index from index_files.collect()
 
   output:
   file "*" into counts_files
 
   script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    }
+  }
 """
-hisat2 -x ${file(file(index[0]).baseName).baseName} -1 ${reads[0]} -2 ${reads[1]} -S ${pair_id}.sam -p ${task.cpus}
+hisat2 -x ${index_id} -1 ${reads[0]} -2 ${reads[1]} -S ${pair_id}.sam -p ${task.cpus}
 """
 }

src/nf_modules/hisat2/mapping_single.config

+profiles {
+  docker {
+    docker.temp = 'auto'
+    docker.enabled = true
+    process {
+      withName: mapping_fastq {
+        cpus = 4
+        container = "hisat2:2.0.0"
+      }
+    }
+  }
+  singularity {
+    singularity.enabled = true
+    process {
+      withName: mapping_fastq {
+        cpus = 4
+        container = "file://bin/hisat2:2.0.0.sif"
+      }
+    }
+  }
+  sge {
+    process{
+      withName: mapping_fastq {
+        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
+        module = "hisat2/2.0.0"
+        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'
+      }
+    }
+  }
+}

src/nf_modules/hisat2/test/mapping_single.nf → src/nf_modules/hisat2/mapping_single.nf

@@ -11,6 +11,7 @@ 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 )
@@ -18,19 +19,24 @@ Channel
   .set { index_files }
 
 process mapping_fastq {
-  tag "$reads.baseName"
-  cpus 4
+  tag "$file_id"
   publishDir "results/mapping/", mode: 'copy'
 
   input:
-  file reads from fastq_files
-  file index from index_files.toList()
+  set file_id, file(reads) from fastq_files
+  file index from index_files.collect()
 
   output:
   file "*" into count_files
 
   script:
+  index_id = index[0]
+  for (index_file in index) {
+    if (index_file =~ /.*\.1\.bt2/ && !(index_file =~ /.*\.rev\.1\.bt2/)) {
+        index_id = ( index_file =~ /(.*)\.1\.bt2/)[0][1]
+    }
+  }
 """
-hisat2 -x ${file(file(index[0]).baseName).baseName} -U ${reads} -S ${reads.baseName}.sam -p ${task.cpus}
+hisat2 -x ${index_id} -U ${reads} -S ${file_id}.sam -p ${task.cpus}
 """
 }