diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 36e7ef46da6b8c3784e916d1ae83bfafe55b8770..220cdce3419562f18858cc73be58157e901dac8d 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 19094c45a0a3c67813ef581f1d388090f57cac8b..e1b0262d050bbf2799ffda390eacb44a1ad7386a 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 7e00b2bc704b289bdcbf31c57f25cd98f4d49061..d24ba5d8a6cdee52b50027ea59b5c639480aab63 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 7e00b2bc704b289bdcbf31c57f25cd98f4d49061..d24ba5d8a6cdee52b50027ea59b5c639480aab63 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 8a373d99e286a3f512d750cf7719de8149e2fb35..98b7cdac14765aea04a052599b22c9e238e9802b 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 704adb6a714cb7b73e79adb96ce78afd28eb911c..7d8e543f0abf1b898484739b99cd26d90166481d 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 704adb6a714cb7b73e79adb96ce78afd28eb911c..7d8e543f0abf1b898484739b99cd26d90166481d 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index d73ff10499cad8c64b5a2553fde8899dbbdff767..89574aa8bd1bb0c3fd658a2e73103a239544048a 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 1c8dfa5d9d3b89ac4e8bc898d2077c283fee2456..4f013608bd6530836ea03c9db9b5c756c78ae385 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ 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 7e6aadec6a8c82d778d7feaddd311d8f675905b6..7317fb7b29a512c9c95c51b7a5792bd1e8aab5e5 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ 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 7e6aadec6a8c82d778d7feaddd311d8f675905b6..7317fb7b29a512c9c95c51b7a5792bd1e8aab5e5 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 28e17285f62db18e4a6cd8034dd27ff959b5de12..f201a5719c6e2d08f17dc3dedc958d5d3a3a441d 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 28e17285f62db18e4a6cd8034dd27ff959b5de12..f201a5719c6e2d08f17dc3dedc958d5d3a3a441d 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ 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 e6d713401dd588ee18b56cc7e45b1fe9d2b7a75d..67a46dc8f55e451dd86e8ea3ce36855ffd68c4b8 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -66,8 +66,6 @@ profiles {
cpus = 1
queue = 'huge'
}
- }
- process{
withName: bam_to_bigwig {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
@@ -82,4 +80,32 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_bam {
+ container = "/sps/lbmc/common/singularity/sambamba:0.6.7.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: bam_to_bigwig {
+ container = "/sps/lbmc/common/singularity/deeptools:3.0.2.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index 0000f5b25a55de4c3d9f29820178e80f55e79f0b..66be28dd24c4092466f55eb15b392b709ab9d2bc 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index afa10d54c3119fe880aed0dba9fdaecc3b5eb841..bb1feb2e709b48911185b75bcfb0e6f6cc23e926 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index f660e797a56ae13b51a02c0d0404989d1ed88fb9..67af9be59231f40d553a13f0eb4c24f87006bf12 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index f660e797a56ae13b51a02c0d0404989d1ed88fb9..67af9be59231f40d553a13f0eb4c24f87006bf12 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 291d2eb44d0a07eb6d0e096c2142e51d78e1aaba..70c9b99628065576415c11f11031fae165185355 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 291d2eb44d0a07eb6d0e096c2142e51d78e1aaba..70c9b99628065576415c11f11031fae165185355 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index fc8ca47b63072365a9069f8806bbdfc4e4a64397..c3784d3132cde31b73bb0d57a3f38f619a4ff0c6 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 31edc5c623bd4532d69ad8454aeaed219a21089e..993ef10b16b725e0e8b00b4abdc7b4c40da6f17b 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 31edc5c623bd4532d69ad8454aeaed219a21089e..993ef10b16b725e0e8b00b4abdc7b4c40da6f17b 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index e703516f3da176c611c4921ca4994ad86fd6823a..7349c5f04d0fc638ae053a8739251120e85ef720 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -74,4 +74,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 755a49b20c6f59da629df35d66c60a4cf0ab3ac3..2599af596033ba29a0df72ba7b6783f1cd107450 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -49,6 +49,23 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 755a49b20c6f59da629df35d66c60a4cf0ab3ac3..2599af596033ba29a0df72ba7b6783f1cd107450 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -49,6 +49,23 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 43e5cbef55973bd71602ac2b2de413a9bc863b22..d5223cd11c15e691b1eb82fb9d51af7b682a65d2 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 4413a1eb819dc1f47cace9f2f9c445d7466463b6..813b55e29eee267f31fc605ae06f2588ce5207dc 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -83,5 +83,22 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index 451cbd2b4d268ae2efa32ea934a8e4f01259b2b6..304ea3e08b400045c9b108a0aa4fb9c7dce0f298 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -82,4 +82,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ 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 b94187533212009fd0f848d3cc10260101193077..64a55bd0b53a335a17a989983501a9417f355852 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -71,41 +71,18 @@ profiles {
ccin2p3_conda {
process{
withName: compute_mappability {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/music/6613c53/:/usr/bin:$PATH"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
withName: music_preprocessing {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/music/6613c53/:/usr/bin:$PATH"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- memory = "10GB"
- time = "24h"
- }
- withName: music_computation {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/music/6613c53/:/usr/bin:$PATH"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- memory = "10GB"
- time = "24h"
- }
- }
- process{
- withName: compute_mappability {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
@@ -117,7 +94,7 @@ profiles {
cpus = 1
queue = 'huge'
}
- withName: music_preprocessing {
+ withName: music_computation {
beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
@@ -129,9 +106,14 @@ profiles {
cpus = 1
queue = 'huge'
}
- withName: music_computation {
- beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
+ }
+ }
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.img"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d551058d409dca24e4629da3d24517ea1846e78e..1149d299a8d52923da7dc6e7aa7369cfc7a92dbb 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 7a3110765e7066243c526e608605e0234865fc40..3519333078b1d0713ddcd42214173fba6eec9718 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 7a3110765e7066243c526e608605e0234865fc40..3519333078b1d0713ddcd42214173fba6eec9718 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index 4b1cab9d149445e9ddd02755483e24e891782db5..7055c98c5be5516493b5ea8d52ac7c7038936e6d 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 20a878c34c75f676dff0aa95f6ab7b6139abcddd..2ccdc387a36f77ae271f39be463023183360170a 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index ed57b7641a6c618a7f4e00cad5eae363158b35f3..57346f105efafc03785ebf517fbd7800bc5a91ed 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index a4ed173205ad6fd9d79ce431b41d7a1965f89e01..6911ff9301e3cf4b1a8a422cf6fdf8d1b2b93378 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 8b6406fc4792384df431ddaaa4e1a14a44ae96c2..0116e7c66ec2a1faf2dd2a6a96acbe5637bacefa 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 9b37acf24f22034181cb59008dda66d7d625f0cc..dfab8d3d1f95a504ebae7a848219e6168a27a29c 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 6f55fb1b71431d5e75f528b31b7513cf9a492cfd..45c69f8ae7b8a381bbe2139dea8cf7525702ec92 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -49,4 +49,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 7d8c883c0e2ad675f3dec2c0834b565f79069f0e..f03bc1a85d2b1e74d0088cade99222d5d6146eaf 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 3bfdaae2c517d4f238fccb649d6035d1da67d249..1538b1a06a35020a5d3ac8cef1824b99555f276d 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -48,4 +48,21 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 143b4b1554d1248b0d683107c4edbdb1f2fb5ca6..2073efc271fba3d71b02dc52aadfbbadf7534125 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -49,5 +49,22 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index c787338fd4d8290245d9f81dc595662441b727fa..e82bd35f96edf31a78c2cd7b62892ec6bb1b367a 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -49,5 +49,22 @@ profiles {
}
}
}
+ ccin2p3 {
+ singularity.enabled = true
+ singularity.runOptions = "--bind /pbs,/sps,/scratch"
+ process{
+ withName: index_fasta {
+ container = "/sps/lbmc/common/singularity/kallisto:0.44.0.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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
+ }
}