nf_modules: fix withname -> withName in config files

src/nf_modules/BWA/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: index_fasta {
+      withName: index_fasta {
         container = "bwa:0.7.17"
       }
     }
   }
   psmn {
     process{
-      withname: index_fasta {
+      withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "BWA/0.7.17"
         executor = "sge"

src/nf_modules/BWA/mapping_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "bwa:0.7.17"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "BWA/0.7.17"
         executor = "sge"

src/nf_modules/Bowtie/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: index_fasta {
+      withName: index_fasta {
         container = "bowtie:1.2.2"
       }
     }
   }
   psmn {
     process{
-      withname: index_fasta {
+      withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie/1.2.2"
         executor = "sge"

src/nf_modules/Bowtie/mapping_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "bowtie:1.2.2"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie/1.2.2:SAMtools/1.7"
         executor = "sge"

src/nf_modules/Bowtie/mapping_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "bowtie:1.2.2"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie/1.2.2:SAMtools/1.7"
         executor = "sge"

src/nf_modules/Bowtie2/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "bowtie2:2.3.4.1"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1"
         executor = "sge"

src/nf_modules/Bowtie2/mapping_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "bowtie2:2.3.4.1"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1:SAMtools/1.7"
         executor = "sge"

src/nf_modules/Bowtie2/mapping_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "bowtie2:2.3.4.1"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "Bowtie2/2.3.4.1:SAMtools/1.7"
         executor = "sge"

src/nf_modules/FastQC/fastqc_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
     }
   }
   psmn {
     process{
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"

src/nf_modules/FastQC/fastqc_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
     }
   }
   psmn {
     process{
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"

src/nf_modules/HTSeq/htseq.config

@@ -3,17 +3,17 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: sort_bam {
+      withName: sort_bam {
         container = "samtools:1.7"
       }
-      withname: counting {
+      withName: counting {
         container = "htseq:0.8.0"
       }
     }
   }
   psmn {
     process{
-      withname: sort_bam {
+      withName: sort_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "SAMtools/1.7"
         executor = "sge"
@@ -22,7 +22,7 @@ profiles {
         time = "12h"
         queue = 'monointeldeb128'
       }
-      withname: trimming {
+      withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "HTSeq/0.8.0"
         executor = "sge"

src/nf_modules/MUSIC/peak_calling_single.config

@@ -3,20 +3,20 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: compute_mappability {
+      withName: compute_mappability {
         container = "music:6613c53"
       }
-      withname: music_preprocessing {
+      withName: music_preprocessing {
         container = "music:6613c53"
       }
-      withname: music_computation {
+      withName: music_computation {
         container = "music:6613c53"
       }
     }
   }
   psmn {
     process{
-      withname: compute_mappability {
+      withName: compute_mappability {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MUSIC/6613c53"
         executor = "sge"
@@ -25,7 +25,7 @@ profiles {
         time = "12h"
         queue = 'monointeldeb128'
       }
-      withname: music_preprocessing {
+      withName: music_preprocessing {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MUSIC/6613c53"
         executor = "sge"
@@ -34,7 +34,7 @@ profiles {
         time = "12h"
         queue = 'monointeldeb128'
       }
-      withname: music_computation {
+      withName: music_computation {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MUSIC/6613c53"
         executor = "sge"

src/nf_modules/MultiQC/multiqc_paired.config

@@ -4,17 +4,17 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
-      withname: multiqc {
+      withName: multiqc {
         container = "multiqc:1.0"
       }
     }
   }
   psmn {
     process{
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"
@@ -25,7 +25,7 @@ profiles {
         pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
-      withname: multiqc {
+      withName: multiqc {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MultiQC/1.0"
         executor = "sge"

src/nf_modules/MultiQC/multiqc_single.config

@@ -3,17 +3,17 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         container = "fastqc:0.11.5"
       }
-      withname: multiqc {
+      withName: multiqc {
         container = "multiqc:1.0"
       }
     }
   }
   psmn {
     process{
-      withname: fastqc_fastq {
+      withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "FastQC/0.11.5"
         executor = "sge"
@@ -24,7 +24,7 @@ profiles {
         pollInterval = '60sec'
         queue = 'monointeldeb128'
       }
-      withname: multiqc {
+      withName: multiqc {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "MultiQC/1.0"
         executor = "sge"

src/nf_modules/RSEM/indexing.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: index_fasta {
+      withName: index_fasta {
         container = "rsem:1.3.0"
       }
     }
   }
   psmn {
     process{
-      withname: index_fasta {
+      withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "RSEM/1.3.0:SAMtools/1.7"
         executor = "sge"

src/nf_modules/RSEM/quantification_paired.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "rsem:1.3.0"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "RSEM/1.3.0:SAMtools/1.7"
         executor = "sge"

src/nf_modules/RSEM/quantification_single.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         container = "rsem:1.3.0"
       }
     }
   }
   psmn {
     process{
-      withname: mapping_fastq {
+      withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "RSEM/1.3.0:SAMtools/1.7"
         executor = "sge"

src/nf_modules/SAMtools/filter_bams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: filter_bam {
+      withName: filter_bam {
         container = "samtools:1.7"
       }
     }
   }
   psmn {
     process{
-      withname: filter_bam {
+      withName: filter_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "SAMtools/1.7"
         executor = "sge"

src/nf_modules/SAMtools/index_bams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: index_bam {
+      withName: index_bam {
         container = "samtools:1.7"
       }
     }
   }
   psmn {
     process{
-      withname: index_bam {
+      withName: index_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "SAMtools/1.7"
         executor = "sge"

src/nf_modules/SAMtools/sort_bams.config

@@ -3,14 +3,14 @@ profiles {
     docker.temp = 'auto'
     docker.enabled = true
     process {
-      withname: sort_bam {
+      withName: sort_bam {
         container = "samtools:1.7"
       }
     }
   }
   psmn {
     process{
-      withname: sort_bam {
+      withName: sort_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
         module = "SAMtools/1.7"
         executor = "sge"