diff --git a/src/nf_modules/BWA/indexing.config b/src/nf_modules/BWA/indexing.config
index 4f9e69761261ed460aecbb3a96aac1bdba98951e..661165009723591e2e246b57d9dc4111c064f280 100644
--- a/src/nf_modules/BWA/indexing.config
+++ b/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
diff --git a/src/nf_modules/BWA/mapping_paired.config b/src/nf_modules/BWA/mapping_paired.config
index d13f1f4e29bb5f84e9263827c6d8d53af5b6cf26..68df48ed2c3070177585837273fbcbb498641dea 100644
--- a/src/nf_modules/BWA/mapping_paired.config
+++ b/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
diff --git a/src/nf_modules/Bowtie/indexing.config b/src/nf_modules/Bowtie/indexing.config
index 64df83d8e77c46983d6222d07bd2469feb7de114..d97a2ad7d12519f4ada498108e133f68f2d0023a 100644
--- a/src/nf_modules/Bowtie/indexing.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/Bowtie/mapping_paired.config b/src/nf_modules/Bowtie/mapping_paired.config
index d2170da748d66e96d4a18b5ba45831c2a31a89c4..fbceecea9563ac290ffdb896e89bfd579316a828 100644
--- a/src/nf_modules/Bowtie/mapping_paired.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/Bowtie/mapping_single.config b/src/nf_modules/Bowtie/mapping_single.config
index d2170da748d66e96d4a18b5ba45831c2a31a89c4..fbceecea9563ac290ffdb896e89bfd579316a828 100644
--- a/src/nf_modules/Bowtie/mapping_single.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/Bowtie2/indexing.config b/src/nf_modules/Bowtie2/indexing.config
index 91abd84d3bc366defa01ae35b5aa77f5d6d2f852..3b87b79e02d9de2de886eede483f16292a6e2b69 100644
--- a/src/nf_modules/Bowtie2/indexing.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/Bowtie2/mapping_paired.config b/src/nf_modules/Bowtie2/mapping_paired.config
index 1f2714a7c2ae69881900232ca269ef349fbffbb6..840c6d430ad41c19d58174e4d148192958c93875 100644
--- a/src/nf_modules/Bowtie2/mapping_paired.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/Bowtie2/mapping_single.config b/src/nf_modules/Bowtie2/mapping_single.config
index 1f2714a7c2ae69881900232ca269ef349fbffbb6..840c6d430ad41c19d58174e4d148192958c93875 100644
--- a/src/nf_modules/Bowtie2/mapping_single.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/FastQC/fastqc_paired.config b/src/nf_modules/FastQC/fastqc_paired.config
index 6e869185a8057c3bc9b0b9f6e13d422f3d7046bd..875a0fc3d8324a42fe058f42df6f5f2cbb1beaee 100644
--- a/src/nf_modules/FastQC/fastqc_paired.config
+++ b/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
diff --git a/src/nf_modules/FastQC/fastqc_single.config b/src/nf_modules/FastQC/fastqc_single.config
index 6e869185a8057c3bc9b0b9f6e13d422f3d7046bd..875a0fc3d8324a42fe058f42df6f5f2cbb1beaee 100644
--- a/src/nf_modules/FastQC/fastqc_single.config
+++ b/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
diff --git a/src/nf_modules/HTSeq/htseq.config b/src/nf_modules/HTSeq/htseq.config
index 6dad8c837205f64ee6021d18158598d88180a53e..42088dd754164acc9065ea8b23c1ba2d5b07b85b 100644
--- a/src/nf_modules/HTSeq/htseq.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/MUSIC/peak_calling_single.config b/src/nf_modules/MUSIC/peak_calling_single.config
index 70375472b84040885a9e827eabf05f09ff0bbb5b..1b53d90d06fe5dcc28f99347770d2c3b3bde8151 100644
--- a/src/nf_modules/MUSIC/peak_calling_single.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/MultiQC/multiqc_paired.config b/src/nf_modules/MultiQC/multiqc_paired.config
index a81a361f557ce60ae47308300bb77bffbb57040d..d43e99bacfc159987feaee082c397ed559af5b23 100644
--- a/src/nf_modules/MultiQC/multiqc_paired.config
+++ b/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
diff --git a/src/nf_modules/MultiQC/multiqc_single.config b/src/nf_modules/MultiQC/multiqc_single.config
index a81a361f557ce60ae47308300bb77bffbb57040d..d43e99bacfc159987feaee082c397ed559af5b23 100644
--- a/src/nf_modules/MultiQC/multiqc_single.config
+++ b/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
diff --git a/src/nf_modules/RSEM/indexing.config b/src/nf_modules/RSEM/indexing.config
index 52ead0dbba140ada3386f3f3f61b453a2c49b374..4822bb0b8febffdf15ade3afa188021d6c3ece24 100644
--- a/src/nf_modules/RSEM/indexing.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/RSEM/quantification_paired.config b/src/nf_modules/RSEM/quantification_paired.config
index ad5c0388ec94ef981ad645900fe2bfc07ce125dc..5c52dce17939d232fd1011b0fce6a2dc27ab0ba5 100644
--- a/src/nf_modules/RSEM/quantification_paired.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/RSEM/quantification_single.config b/src/nf_modules/RSEM/quantification_single.config
index ad5c0388ec94ef981ad645900fe2bfc07ce125dc..5c52dce17939d232fd1011b0fce6a2dc27ab0ba5 100644
--- a/src/nf_modules/RSEM/quantification_single.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/SAMtools/filter_bams.config b/src/nf_modules/SAMtools/filter_bams.config
index cee59e8bc0d9cefaf7fbaff250113df002c64662..15692631cde16131484c5cd2ae10edc1f2c3db97 100644
--- a/src/nf_modules/SAMtools/filter_bams.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/SAMtools/index_bams.config b/src/nf_modules/SAMtools/index_bams.config
index 040fee577b0ddd545443c55eeb5ec31ac2bf44f1..277e0a36fed8be041f1fa6167dc10aa588392223 100644
--- a/src/nf_modules/SAMtools/index_bams.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/SAMtools/sort_bams.config b/src/nf_modules/SAMtools/sort_bams.config
index 20dcdccf4af24e2af0a7cc39f5ef935b02b998cc..d961965c545f7621370e94a2c6c6f5cd9e50e5ba 100644
--- a/src/nf_modules/SAMtools/sort_bams.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/SAMtools/split_bams.config b/src/nf_modules/SAMtools/split_bams.config
index 503d553953924d07b728142bd16f9e8ce8b33ca2..43cba89e1eed80e0bd3c14bc8e7c0329ce861ba3 100644
--- a/src/nf_modules/SAMtools/split_bams.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/SRAtoolkit/fastqdump.config b/src/nf_modules/SRAtoolkit/fastqdump.config
index 1c29984a4f8d2f283445c29ee624dcd7b38cf173..9fb28f952ccd9825f16850e98c1ebf8b49deac3b 100644
--- a/src/nf_modules/SRAtoolkit/fastqdump.config
+++ b/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
diff --git a/src/nf_modules/UrQt/urqt.config b/src/nf_modules/UrQt/urqt.config
index e08a434ad2b9f8e27cd95df6ce0324b776c69104..6f2dc8fba8fc579fa59eabba55bec2fd90ccceb1 100644
--- a/src/nf_modules/UrQt/urqt.config
+++ b/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
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index cf0c5c7d2c20812516e325382cac02854b66dcfc..2e4192153e34aeaa01db3e92f70311fd1e9c6ef0 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 1303bd685a5a5b815f3fbc46e5983e632fabeecb..041a7c7a1cc1fafa7571d647f35aedddea20ae6b 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index c6d211c6d30602ac2a1d21d9ebf6db5375781989..1f10cb454a71c71bf845ad7624eab9907126e2c1 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/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"
       }
     }
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 47ab19e1509b567d2b39af149d6a59be03f58be3..646ecb8ea30e023d99053858ddb0b0ff451b1fd9 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/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"
       }
     }
diff --git a/src/training_dataset.config b/src/training_dataset.config
index 1fb6161075464de356df5fc0cc47d46cde22f164..3bddf5fc6da7e04df7e4bea364adc31d109fe4d4 100644
--- a/src/training_dataset.config
+++ b/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"
       }
     }