diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 41c1dac9c0b9d177d14fb72448668a007935751d..1a2252127e23a53e0511cc743b1233ec5d558b33 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fasta_from_bed {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 73217f9acad643d3e4f6ddec51ae86ab0af77f21..06b57209094a1f13ef56cec8174cc5249430014d 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 44ab8bcbae3895d5671ecff3d641f3b6a405fb85..61f40f9e4b7bdacd779a26ee496001d84bf5e18e 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 44ab8bcbae3895d5671ecff3d641f3b6a405fb85..61f40f9e4b7bdacd779a26ee496001d84bf5e18e 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 20487563f1931d316ddd4ea266f33ef21a7fae51..2d52dc48f5523e18a7b803374d0d28be55f99b55 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 7874ae45bd8965e6d763a48d79eb1424b11b3bb6..85655e48219db38ca8e2e21c7851ada62ebe9f20 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 7874ae45bd8965e6d763a48d79eb1424b11b3bb6..85655e48219db38ca8e2e21c7851ada62ebe9f20 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 72274ad40def0a40ced26cbe604a8890051c604f..c970b5bbc084e90662d9af3766db67d40a6dcc8c 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index a3e5c6282833019f29879ac01d3b450e819633e2..af4f9683709cbe62745472fbc14d49451e1cfb09 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index e58c385a19462b9ffe19816ee1e3e68599c5f47e..8add46ca97a05ec35723d7a481bd4ed4b0870a19 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index e58c385a19462b9ffe19816ee1e3e68599c5f47e..8add46ca97a05ec35723d7a481bd4ed4b0870a19 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: adaptor_removal {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 9b49fcee87d3de5d362d861671de26f326d711ed..721d88051a7106d01eb57308460d0c27a8df40a2 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
@@ -58,8 +57,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 9b49fcee87d3de5d362d861671de26f326d711ed..721d88051a7106d01eb57308460d0c27a8df40a2 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
@@ -58,8 +57,7 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 67a46dc8f55e451dd86e8ea3ce36855ffd68c4b8..5be6a4cbeff21f70c6ccb314b7ded8e03af73b9d 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -26,7 +26,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -61,8 +61,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -73,8 +73,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -90,8 +90,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -101,8 +101,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index fb1cd0483b4d9a7a9192e11696c1a93149c5af45..b09867699daf264e2b5c33d103243cf7f4d30e82 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: compute_matrix {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 08d20977b90e7395f3e4691aa420d1ef96fd23a5..e9fe1504b5f9dc17d337ea04a5c16240820653d9 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: plot_profile {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 7d9c83e45cf27d1819728e34818179a281756d1e..df041cb9df4262756b3701b9b291419abd88a643 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastp_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 7d9c83e45cf27d1819728e34818179a281756d1e..df041cb9df4262756b3701b9b291419abd88a643 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastp_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 6e9dcaf7a72af01b35500485568cf0b15886b0aa..2ed15c542eef76cc7c0ed7fdcaa9ce9bc6dc4613 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 6e9dcaf7a72af01b35500485568cf0b15886b0aa..2ed15c542eef76cc7c0ed7fdcaa9ce9bc6dc4613 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 6d39e60ac10ae949693ac487b996e731cb7acf74..d97e7c7490044ab754a995d30fd949d40306e827 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 97b4807dc83054b2bd17a31205887e7ebe408141..c0b9c8085f558a6733b001b339565dbc40a57ac3 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 97b4807dc83054b2bd17a31205887e7ebe408141..c0b9c8085f558a6733b001b339565dbc40a57ac3 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 09b368ae47a9f29ad42cc7ae6a0f2dae548034e6..c8f844e9fb366728e47bcb79c6a13c266fa29310 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -22,7 +22,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -55,8 +55,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -67,8 +67,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -84,8 +84,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -95,8 +95,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 84722f6daee159d986a7eafbfb0e7d29f6cfe8fd..b677b616e70579432463360369e9f7bfd45ee305 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 801dfdc17bcba182fc6894b07ce55c1eeb03dc03..620e506d463f56e03aa9baaa566037dda1a047f6 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 801dfdc17bcba182fc6894b07ce55c1eeb03dc03..620e506d463f56e03aa9baaa566037dda1a047f6 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 93697c70ce2f6179f5ec8ac4f39ce6ca6b3acf6a..8e3965f8666807fe531eb0ad2d005aa4000e5442 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: peak_calling {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 86ead2c4f4a1a29e1164b7ea5ab870cead90f496..1825a1355594ec0cc3aadbd8007f4cf271a3ba67 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -27,7 +27,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -64,8 +64,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -76,8 +76,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -93,8 +93,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -104,8 +104,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index e296853fb7d7addfbfc1e22a6c483a85b9ac8427..6a2edfb6a7f3b2349ac4042ca94b0bdd44aa8a33 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -26,7 +26,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastqc_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -63,8 +63,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -75,8 +75,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -92,8 +92,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -103,8 +103,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 972de3d7961ba73e4a38521e940a3a9891e1525a..dc46d8c8281d8ce74a2ff2733df4864ec33e1529 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -11,7 +11,7 @@ profiles {
container = "music:6613c53"
cpus = 1
}
- withName: music_computation {
+ withName: music_computation{
container = "music:6613c53"
cpus = 1
}
@@ -28,13 +28,13 @@ profiles {
container = "file://bin/music:6613c53.img"
cpus = 1
}
- withName: music_computation {
+ withName: music_computation{
container = "file://bin/music:6613c53.img"
cpus = 1
}
}
}
- psmn {
+ psmn{
process{
withName: compute_mappability {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -56,7 +56,7 @@ profiles {
time = "12h"
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
- withName: music_computation {
+ withName: music_computation{
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "music/6613c53"
executor = "sge"
@@ -77,8 +77,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -89,20 +89,20 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
- withName: music_computation {
+ withName: music_computation{
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -118,8 +118,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -129,19 +129,19 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
- withName: music_computation {
+ withName: music_computation{
container = "/sps/lbmc/common/singularity/music:6613c53.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index b9de25369f632eaf3607339be219a9d0667feb3e..d58a310d88e5d160f597f15afc884b4dcc10fcec 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_fasta {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 03152ccaf28ebc6aa76e6f4f2dd582913ce169f7..75aae6edaa335d8a0cc1f6405b0c35d4be1800d8 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 03152ccaf28ebc6aa76e6f4f2dd582913ce169f7..75aae6edaa335d8a0cc1f6405b0c35d4be1800d8 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: mapping_fastq {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index cb3d4308e153f4bdea2d63bc41b359e679e8a6f6..9199b7a4d958830dddd269764ceebc0d0993def3 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index de2eb6e80e9ed05d755792b76af0c07d5cbc328e..0a71fc389f479c3597b7cf53751348aab7e70448 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 74dd96d055ea9b6a61a8e0851b85e824c71cca57..8a3e4ab57c962728c577778a1f155e69ce8e60c3 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index a47c35ac6a744507e7ea68e577e1b45484b0163a..7fd05167e1565fdd54716481d08e970172dc1a72 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: dedup_sam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index dfc5d68f5b6202ec40f72e7b1ce1da51be617bc4..fc7a216c9a8bb175a4a427ead760d1e32e30bf56 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: filter_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 3c0e876cfb9a4636221c5eb9fe21873ecec393cd..8b910b604136284756c752065f49a8c1705ddaa7 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: index_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 690dc9038c4c13cd9d71bc3f835bb844ab391396..d5e06e31e6ee28efd21c698133604e0cb5188b1f 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: sort_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 6afd888004da99b66fd6125e38d6b10b4fa59eb5..c145bf33c4441a84c413eeba43dcce45ea2a5c1e 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: split_bam {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 6abc3955f8ee8a8ed1c603978b916ca4c142afad..0d5acb9f7eda6159f06cb548a98c4b5248dd0685 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: fastq_dump {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -41,8 +41,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -58,8 +58,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 976921f2975f502092589e07156b1c5080c14030..dbe4e11ccc1d77caf8fa3f346c344eeca27ae4f7 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index 99fb7d9465afa3ca4245ba002062d08ae90af0e8..016d65033739a5b850f368ef00a98c94a513f449 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -18,7 +18,7 @@ profiles {
}
}
}
- psmn {
+ psmn{
process{
withName: trimming {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
@@ -42,8 +42,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}
@@ -59,8 +59,8 @@ profiles {
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o ~/logs/ -e ~/logs/"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n\
+ "
cpus = 1
queue = 'huge'
}