nf config file update nf syntax for process

src/nf_modules/SAMtools/split_bams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $split_bam {
+      withname: split_bam {
         container = "samtools:1.7"
       }
     }
   }
   psmn {
     process{
-      $split_bam {
+      withname: split_bam {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
     }

src/nf_modules/SRAtoolkit/fastqdump.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $fastq_dump {
+      withname: fastq_dump {
         container = "sratoolkit:2.8.2"
       }
     }
   }
   psmn {
     process{
-      $fastq_dump {
+      withname: fastq_dump {
         beforeScript = "module purge; module load SRAtoolkit/2.8.2"
         executor = "psmn"
         cpus = 1

src/nf_modules/UrQt/urqt.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $trimming {
+      withname: trimming {
         container = "urqt:d62c1f8"
       }
     }
   }
   psmn {
     process{
-      $trimming {
+      withname: trimming {
         beforeScript = "module purge; module load UrQt/d62c1f8"
         executor = "psmn"
         cpus = 4

src/nf_modules/sambamba/index_bams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_bam {
+      withname: index_bam {
         container = "sambamba:0.6.7"
       }
     }
   }
   psmn {
     process{
-      $index_bam {
+      withname: index_bam {
         beforeScript = "module purge; module load sambamba/0.6.7"
       }
     }

src/nf_modules/sambamba/sort_bams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $sort_bam {
+      withname: sort_bam {
         container = "sambamba:0.6.7"
       }
     }
   }
   psmn {
     process{
-      $sort_bam {
+      withname: sort_bam {
         beforeScript = "module purge; module load sambamba/0.6.7"
       }
     }

src/nf_modules/sambamba/split_bams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $split_bam {
+      withname: split_bam {
         container = "sambamba:0.6.7"
       }
     }
   }
   psmn {
     process{
-      $split_bam {
+      withname: split_bam {
         beforeScript = "module purge; module load sambamba/0.6.7"
       }
     }

src/nf_modules/samblaster/dedup_sams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $dedup_sam {
+      withname: dedup_sam {
         container = "samblaster:0.1.24"
       }
     }
   }
   psmn {
     process{
-      $dedup_sam {
+      withname: dedup_sam {
         beforeScript = "module purge; module load samblaster/0.1.24"
       }
     }

src/training_dataset.config

@@ -3,44 +3,44 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $build_synthetic_bed {
+      withname: build_synthetic_bed {
         container = "bedtools:2.25.0"
       }
-      $fasta_from_bed {
+      withname: fasta_from_bed {
         container = "bedtools:2.25.0"
       }
-      $index_fasta {
+      withname: index_fasta {
         container = "bowtie2:2.3.4.1"
       }
-      $mapping_fastq_paired {
+      withname: mapping_fastq_paired {
         container = "bowtie2:2.3.4.1"
       }
-      $bam_2_fastq_paired {
+      withname: bam_2_fastq_paired {
         container = "samtools:1.7"
       }
-      $sort_bam_paired {
+      withname: sort_bam_paired {
         container = "samtools:1.7"
       }
-      $index_bam_paired {
+      withname: index_bam_paired {
         container = "samtools:1.7"
       }
-      $mapping_fastq_single {
+      withname: mapping_fastq_single {
         container = "bowtie2:2.3.4.1"
       }
-      $bam_2_fastq_single {
+      withname: bam_2_fastq_single {
         container = "samtools:1.7"
       }
-      $sort_bam_single {
+      withname: sort_bam_single {
         container = "samtools:1.7"
       }
-      $index_bam_single {
+      withname: index_bam_single {
         container = "samtools:1.7"
       }
     }
   }
   psmn {
     process{
-      $build_synthetic_bed {
+      withname: build_synthetic_bed {
         beforeScript = "module purge; module load BEDtools/2.25.0"
         executor = "psmn"
         cpus = 1
@@ -51,7 +51,7 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-      $fasta_from_bed {
+      withname: fasta_from_bed {
         beforeScript = "module purge; module load BEDtools/2.25.0"
         executor = "psmn"
         cpus = 1
@@ -62,31 +62,31 @@ profiles {
         queue = 'h6-E5-2667v4deb128'
         penv = 'openmp8'
       }
-      $index_fasta {
+      withname: index_fasta {
         beforeScript = "module purge; module load Bowtie2/2.3.4.1"
       }
-      $mapping_fastq_paired {
+      withname: mapping_fastq_paired {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
       }
-      $bam_2_fastq_paired {
+      withname: bam_2_fastq_paired {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
-      $sort_bam_paired {
+      withname: sort_bam_paired {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
-      $index_bam_paired {
+      withname: index_bam_paired {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
-      $mapping_fastq_single {
+      withname: mapping_fastq_single {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
       }
-      $bam_2_fastq_single {
+      withname: bam_2_fastq_single {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
-      $sort_bam_single {
+      withname: sort_bam_single {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
-      $index_bam_single {
+      withname: index_bam_single {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
     }