nf_modules: update config files to match psmn lowercase module names

src/nf_modules/bedtools/fasta_from_bed.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: fasta_from_bed {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "BEDtools/2.25.0"
+        module = "bedtools/2.25.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/bowtie/indexing.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Bowtie/1.2.2"
+        module = "bowtie/1.2.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/bowtie/mapping_paired.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Bowtie/1.2.2:SAMtools/1.7"
+        module = "bowtie/1.2.2:samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16

src/nf_modules/bowtie/mapping_single.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Bowtie/1.2.2:SAMtools/1.7"
+        module = "bowtie/1.2.2:samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16

src/nf_modules/bowtie2/indexing.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Bowtie2/2.3.4.1"
+        module = "bowtie2/2.3.4.1"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16

src/nf_modules/bowtie2/mapping_paired.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+        module = "bowtie2/2.3.4.1:samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16

src/nf_modules/bowtie2/mapping_single.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Bowtie2/2.3.4.1:SAMtools/1.7"
+        module = "bowtie2/2.3.4.1:samtools/1.7"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16

src/nf_modules/bwa/indexing.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "BWA/0.7.17"
+        module = "bwa/0.7.17"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16

src/nf_modules/bwa/mapping_paired.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "BWA/0.7.17"
+        module = "bwa/0.7.17"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 16

src/nf_modules/deeptools/bam_to_bigwig.config

@@ -25,7 +25,7 @@ profiles {
       }
       withName: bam_to_bigwig {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deepTools/3.0.2"
+        module = "deeptools/3.0.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/deeptools/compute_matrix.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: compute_matrix {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deepTools/3.0.2"
+        module = "deeptools/3.0.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/deeptools/plot_profile.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: plot_profile {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deepTools/3.0.2"
+        module = "deeptools/3.0.2"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/fastqc/fastqc_paired.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "FastQC/0.11.5"
+        module = "fastqc/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1

src/nf_modules/fastqc/fastqc_single.config

@@ -22,7 +22,7 @@ profiles {
     process{
       withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "FastQC/0.11.5"
+        module = "fastqc/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         cpus = 1

src/nf_modules/htseq/htseq.config

@@ -15,7 +15,7 @@ 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"
@@ -24,7 +24,7 @@ profiles {
       }
       withName: trimming {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "HTSeq/0.8.0"
+        module = "htseq/0.8.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "20GB"

src/nf_modules/kallisto/indexing.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: index_fasta {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Kallisto/0.44.0"
+        module = "kallisto/0.44.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/kallisto/mapping_paired.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Kallisto/0.44.0"
+        module = "kallisto/0.44.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/kallisto/mapping_single.config

@@ -12,7 +12,7 @@ profiles {
     process{
       withName: mapping_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "Kallisto/0.44.0"
+        module = "kallisto/0.44.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "30GB"

src/nf_modules/multiqc/multiqc_paired.config

@@ -16,7 +16,7 @@ profiles {
     process{
       withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "FastQC/0.11.5"
+        module = "fastqc/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "5GB"
@@ -27,7 +27,7 @@ profiles {
       }
       withName: multiqc {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "MultiQC/1.0"
+        module = "multiqc/1.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "5GB"

src/nf_modules/multiqc/multiqc_single.config

@@ -15,7 +15,7 @@ profiles {
     process{
       withName: fastqc_fastq {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "FastQC/0.11.5"
+        module = "fastqc/0.11.5"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "5GB"
@@ -26,7 +26,7 @@ profiles {
       }
       withName: multiqc {
         beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "MultiQC/1.0"
+        module = "multiqc/1.0"
         executor = "sge"
         clusterOptions = "-m e -cwd -V"
         memory = "5GB"