nf_modules: update config files to match psmn lowercase module names

src/nf_modules/music/peak_calling_single.config

@@ -18,7 +18,7 @@ profiles {
     process{
       withName: compute_mappability {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "MUSIC/6613c53"
+        module = "music/6613c53"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"
@@ -27,7 +27,7 @@ profiles {
       }
       withName: music_preprocessing {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "MUSIC/6613c53"
+        module = "music/6613c53"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"
@@ -36,7 +36,7 @@ profiles {
       }
       withName: music_computation {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "MUSIC/6613c53"
+        module = "music/6613c53"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/rsem/indexing.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "RSEM/1.3.0:SAMtools/1.7"
+        module = "rsem/1.3.0:samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/rsem/quantification_paired.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "RSEM/1.3.0:SAMtools/1.7"
+        module = "rsem/1.3.0:samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/rsem/quantification_single.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "RSEM/1.3.0:SAMtools/1.7"
+        module = "rsem/1.3.0:samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/samtools/filter_bams.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: filter_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "SAMtools/1.7"
+        module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/samtools/index_bams.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: index_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "SAMtools/1.7"
+        module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/samtools/sort_bams.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: sort_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "SAMtools/1.7"
+        module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/samtools/split_bams.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: split_bam {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "SAMtools/1.7"
+        module = "samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/sratoolkit/fastqdump.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: fastq_dump {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "SRAtoolkit/2.8.2"
+        module = "sratoolkit/2.8.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/urqt/trimming_paired.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "UrQt/d62c1f8"
+        module = "urqt/d62c1f8"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "5GB"

src/nf_modules/urqt/trimming_single.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "UrQt/d62c1f8"
+        module = "urqt/d62c1f8"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16