nf config file update nf syntax for process

src/nf_modules/BWA/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_fasta {
+      withname: index_fasta {
         container = "bwa:0.7.17"
       }
     }
   }
   psmn {
     process{
-      $index_fasta {
+      withname: index_fasta {
         beforeScript = "module purge; module load BWA/0.7.17"
         executor = "psmn"
         cpus = 1

src/nf_modules/BWA/mapping_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withname: mapping_fastq {
         container = "bwa:0.7.17"
       }
     }
   }
   psmn {
     process{
-      $mapping_fastq {
+      withname: mapping_fastq {
         beforeScript = "module purge; module load BWA/0.7.17"
         executor = "psmn"
         cpus = 4

src/nf_modules/Bowtie/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_fasta {
+      withname: index_fasta {
         container = "bowtie:1.2.2"
       }
     }
   }
   psmn {
     process{
-      $index_fasta {
+      withname: index_fasta {
         beforeScript = "module purge; module load Bowtie/1.2.2"
       }
     }

src/nf_modules/Bowtie/mapping_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withname: mapping_fastq {
         container = "bowtie:1.2.2"
       }
     }
   }
   psmn {
     process{
-      $mapping_fastq {
+      withname: mapping_fastq {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
       }
     }

src/nf_modules/Bowtie/mapping_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withname: mapping_fastq {
         container = "bowtie:1.2.2"
       }
     }
   }
   psmn {
     process{
-      $mapping_fastq {
+      withname: mapping_fastq {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie/1.2.2"
       }
     }

src/nf_modules/Bowtie2/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_fasta {
+      withname: index_fasta {
         container = "bowtie2:2.3.4.1"
       }
     }
   }
   psmn {
     process{
-      $index_fasta {
+      withname: index_fasta {
         beforeScript = "module purge; module load Bowtie2/2.3.4.1"
       }
     }

src/nf_modules/Bowtie2/mapping_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withname: mapping_fastq {
         container = "bowtie2:2.3.4.1"
       }
     }
   }
   psmn {
     process{
-      $mapping_fastq {
+      withname: mapping_fastq {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
       }
     }

src/nf_modules/Bowtie2/mapping_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withname: mapping_fastq {
         container = "bowtie2:2.3.4.1"
       }
     }
   }
   psmn {
     process{
-      $mapping_fastq {
+      withname: mapping_fastq {
         beforeScript = "module purge; module load SAMtools/1.7; module load Bowtie2/2.3.4.1"
       }
     }

src/nf_modules/FastQC/fastqc_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
     }
   }
   psmn {
     process{
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         beforeScript = "module purge; module load FastQC/0.11.5"
         executor = "psmn"
         cpus = 1

src/nf_modules/FastQC/fastqc_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
     }
   }
   psmn {
     process{
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         beforeScript = "module purge; module load FastQC/0.11.5"
         executor = "psmn"
         cpus = 1

src/nf_modules/HTSeq/htseq.config

@@ -3,20 +3,20 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $sort_bam {
+      withname: sort_bam {
         container = "samtools:1.7"
       }
-      $counting {
+      withname: counting {
         container = "htseq:0.8.0"
       }
     }
   }
   psmn {
     process{
-      $sort_bam {
+      withname: sort_bam {
         beforeScript = "module purge; module load SAMtools/1.7"
       }
-      $trimming {
+      withname: trimming {
         beforeScript = "module purge; module load HTSeq/0.8.0"
       }
     }

src/nf_modules/MUSIC/peak_calling_single.config

@@ -3,26 +3,26 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $compute_mappability {
+      withname: compute_mappability {
         container = "music:6613c53"
       }
-      $music_preprocessing {
+      withname: music_preprocessing {
         container = "music:6613c53"
       }
-      $music_computation {
+      withname: music_computation {
         container = "music:6613c53"
       }
     }
   }
   psmn {
     process{
-      $compute_mappability {
+      withname: compute_mappability {
         beforeScript = "module purge; module load MUSIC/6613c53"
       }
-      $music_preprocessing {
+      withname: music_preprocessing {
         beforeScript = "module purge; module load MUSIC/6613c53"
       }
-      $music_computation {
+      withname: music_computation {
         beforeScript = "module purge; module load MUSIC/6613c53"
       }
     }

src/nf_modules/MultiQC/multiqc_paired.config

@@ -3,17 +3,17 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
-      $multiqc {
+      withname: multiqc {
         container = "multiqc:1.0"
       }
     }
   }
   psmn {
     process{
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         beforeScript = "module purge; module load FastQC/0.11.5"
         executor = "psmn"
         cpus = 1
@@ -23,7 +23,7 @@ profiles {
         pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
-      $multiqc {
+      withname: multiqc {
         beforeScript = "module purge; module load FastQC/1.0"
         executor = "psmn"
         cpus = 1

src/nf_modules/MultiQC/multiqc_single.config

@@ -3,17 +3,17 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
-      $multiqc {
+      withname: multiqc {
         container = "multiqc:1.0"
       }
     }
   }
   psmn {
     process{
-      $fastqc_fastq {
+      withname: fastqc_fastq {
         beforeScript = "module purge; module load FastQC/0.11.5"
         executor = "psmn"
         cpus = 1
@@ -23,7 +23,7 @@ profiles {
         pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
-      $multiqc {
+      withname: multiqc {
         beforeScript = "module purge; module load FastQC/1.0"
         executor = "psmn"
         cpus = 1

src/nf_modules/RSEM/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $index_fasta {
+      withname: index_fasta {
         container = "rsem:1.3.0"
       }
     }
   }
   psmn {
     process{
-      $index_fasta {
+      withname: index_fasta {
         beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
       }
     }

src/nf_modules/RSEM/quantification_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withname: mapping_fastq {
         container = "rsem:1.3.0"
       }
     }
   }
   psmn {
     process{
-      $mapping_fastq {
+      withname: mapping_fastq {
         beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
       }
     }

src/nf_modules/RSEM/quantification_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      $mapping_fastq {
+      withname: mapping_fastq {
         container = "rsem:1.3.0"
       }
     }
   }
   psmn {
     process{
-      $mapping_fastq {
+      withname: mapping_fastq {
         beforeScript = "module purge; module load RSEM/1.3.0; module load SAMtools/1.7"
       }
     }

src/nf_modules/SAMtools/filter_bams.config

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

src/nf_modules/SAMtools/index_bams.config

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

src/nf_modules/SAMtools/sort_bams.config

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