diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config index 5311e9f5e5d568c655a4ac17f167ea2799c1a704..c1ac99f140dd3d71c0d592432ef1666ff52fc25b 100644 --- a/src/nf_modules/bedtools/fasta_from_bed.config +++ b/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" diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config index 5e9d8233d5a3ecca55917ed267906b6e89c941c7..9ae43af607f44e01f77b0b75970cfc1c5f419151 100644 --- a/src/nf_modules/bowtie/indexing.config +++ b/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" diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config index b27917e1733811b53cc69a2e8553dbfb58e4abad..e516bc308afa4193e6926832637ade2ce9cf59af 100644 --- a/src/nf_modules/bowtie/mapping_paired.config +++ b/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 diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config index b27917e1733811b53cc69a2e8553dbfb58e4abad..e516bc308afa4193e6926832637ade2ce9cf59af 100644 --- a/src/nf_modules/bowtie/mapping_single.config +++ b/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 diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config index c53d855a63f599cad802c3f12e0114c875bd3ee5..0589f4dddba99e7aeff7e04b69eaa50add3a9260 100644 --- a/src/nf_modules/bowtie2/indexing.config +++ b/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 diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config index 27933c3bf5582ae32fc7012598e8f05bb642a09b..eee236b705f89e5b73678c89625838205d40975c 100644 --- a/src/nf_modules/bowtie2/mapping_paired.config +++ b/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 diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config index 27933c3bf5582ae32fc7012598e8f05bb642a09b..eee236b705f89e5b73678c89625838205d40975c 100644 --- a/src/nf_modules/bowtie2/mapping_single.config +++ b/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 diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config index 367e0dfdc90a4b3a32241fed08459b1cfc3a9fa4..aa5967bebc0c42ea903fb003b89e1808b8348501 100644 --- a/src/nf_modules/bwa/indexing.config +++ b/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 diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config index 5535fd104b1b62d933c6dcfed34e2d6364fd5503..e71fc9494c6ce5c5b234ae0efae82ddcb15e8527 100644 --- a/src/nf_modules/bwa/mapping_paired.config +++ b/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 diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config index c1b71cb03cf2962ada6ab81428371f9dc8fc8b8d..ab28edcb57900abc1f77900e2e76a7a1fad19dd0 100644 --- a/src/nf_modules/deeptools/bam_to_bigwig.config +++ b/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" diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config index 27e63ca63b6136955ae86f0f9063a7f827a4db4f..7159cbc7bff8bec00caee83ec53e415ecb51a5b1 100644 --- a/src/nf_modules/deeptools/compute_matrix.config +++ b/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" diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config index 4a94d1de938c381cd57e249793d0430b95e59def..984575cc24a3b7a001a91d5c7fe096c7b17fd284 100644 --- a/src/nf_modules/deeptools/plot_profile.config +++ b/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" diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config index 94baaa284d4f7fb4969bbc5be2f0daee0199a074..78abe9278d56f0e8610c4865b6e7ce4d5c23a601 100644 --- a/src/nf_modules/fastqc/fastqc_paired.config +++ b/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 diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config index 94baaa284d4f7fb4969bbc5be2f0daee0199a074..78abe9278d56f0e8610c4865b6e7ce4d5c23a601 100644 --- a/src/nf_modules/fastqc/fastqc_single.config +++ b/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 diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config index 87368e139794cfdbb8c577f657e2ecbee0871479..94fe2781667a280f45e06abb982e6fb0fcbab84f 100644 --- a/src/nf_modules/htseq/htseq.config +++ b/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" diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config index c52f9b5111aa45727e2b8f3d49a2738aadc06233..8e7131291f896159235d13d48786412a34f3cdea 100644 --- a/src/nf_modules/kallisto/indexing.config +++ b/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" diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config index 2274d13dab4c777b2c25f50617d92f8aeb606379..a0ec051d1c2a3300aae241dbccfc36bdc06a9f85 100644 --- a/src/nf_modules/kallisto/mapping_paired.config +++ b/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" diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config index 2274d13dab4c777b2c25f50617d92f8aeb606379..a0ec051d1c2a3300aae241dbccfc36bdc06a9f85 100644 --- a/src/nf_modules/kallisto/mapping_single.config +++ b/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" diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config index 592b63c23d50b1e541e7bf981f5e41e2e71ebd03..323e81d2ebfc1570109cd9013280f5bd43ec82b6 100644 --- a/src/nf_modules/multiqc/multiqc_paired.config +++ b/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" diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config index 7f6bf3d94940eece66b6febd9f2313b43e4236d0..a7f3e82e016ef440f78921408ef865ae1d386b8a 100644 --- a/src/nf_modules/multiqc/multiqc_single.config +++ b/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" diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config index 2d7145ae1ff375606278d855a02587f069ff6d13..f9a1d7991fda7f0887a2a6b71617cb0039048463 100644 --- a/src/nf_modules/music/peak_calling_single.config +++ b/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" diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config index c0d3287e2e2de4e96ab8d188511bf44bb0c538cb..059dbbaa49253c00a1e82fcd0cb6dd2b4802234c 100644 --- a/src/nf_modules/rsem/indexing.config +++ b/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" diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config index 46ff1549641ae6bca4429b0c4f880c01d3479039..16de29e87a153f7cd1e95ea7c1bd7e6391d1cfaa 100644 --- a/src/nf_modules/rsem/quantification_paired.config +++ b/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" diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config index 46ff1549641ae6bca4429b0c4f880c01d3479039..16de29e87a153f7cd1e95ea7c1bd7e6391d1cfaa 100644 --- a/src/nf_modules/rsem/quantification_single.config +++ b/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" diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config index ef3aa49103b3e1181ed5164974f089c2467bf05f..36d191dc499b3fdbd32f4d1bef4845d38e3ac50c 100644 --- a/src/nf_modules/samtools/filter_bams.config +++ b/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" diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config index 135b6b3a98579e4d7aca56c75699be13121cb93b..fc6122c9c5f11d894722dea126289c8b6e29fec7 100644 --- a/src/nf_modules/samtools/index_bams.config +++ b/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" diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config index 1c1bdca5a5f1f60e786564e9ae40f333cb11f0c9..0071ca2c33e6ae6d8240cff376f2eaea84e46285 100644 --- a/src/nf_modules/samtools/sort_bams.config +++ b/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" diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config index 15880281e363b4de61a362ffe6bc67bba704242f..e2d521cefc24944cdc2a760cd77842fe0dd1004f 100644 --- a/src/nf_modules/samtools/split_bams.config +++ b/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" diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config index 67676b9ad635f80b8973db656ba43de1635bd39e..ef335129858460c7ab291afe9935c3feeae20a35 100644 --- a/src/nf_modules/sratoolkit/fastqdump.config +++ b/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" diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config index c2b4e3f68aa0432a8d704202a3572334fae03b2e..ce5d57365e9f306b15b32cc39560095605aafab3 100644 --- a/src/nf_modules/urqt/trimming_paired.config +++ b/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" diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config index b102d8bd2700ad0885179efa787ea3e457835368..74503ba16dab84c174e7bcb2a6fe9488ded26d21 100644 --- a/src/nf_modules/urqt/trimming_single.config +++ b/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