diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index eed7325870c38ba8453ea1090c02c8c879c5752f..17dee4b14b8ad9e56706506d0351ca31324c0052 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fasta_from_bed {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bedtools/2.25.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bedtools_2.25.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 10c4ac96364c0093537f963b9b565c16e769465a..627cc943b698862f28c2182673d311958726902a 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
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'
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index f531d0dcedcfce5e6233e0f41d4a2f43c9810fbb..598b99a1706fa751c2fe6cec668ec08b192ac2b5 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index f531d0dcedcfce5e6233e0f41d4a2f43c9810fbb..598b99a1706fa751c2fe6cec668ec08b192ac2b5 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie/1.2.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
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'
}
}
}
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 80de2148b072dbf77ba3974b2acc7c6fc08dba56..966b7a9f9a238627809c670e1d00c02226e65d97 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 44adb9a536af636e5f70f6d664fc4d49ed3f4c03..5c975a8c7d2405745546477466b99b134df3b3cf 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
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'
}
}
}
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 44adb9a536af636e5f70f6d664fc4d49ed3f4c03..5c975a8c7d2405745546477466b99b134df3b3cf 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bowtie2/2.3.4.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index a6e6d9fe38e87a692f606bca6568c51a613cd5bf..eeb59fad260a079e53e9d882fecfbf3aba4c9707 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
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'
}
}
}
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index d583ff1cbaa45f8853e43fef543e8e2daf0c44ce..7b96412036b71dd7aaa115fda671b55317ffede6 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/bwa/0.7.17/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index f7d0ebbdb2fb668a70894ce35fcad6130a001245..6fb8ea642ba26510126f59066303db015fb9b068 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
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'
}
}
}
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index f7d0ebbdb2fb668a70894ce35fcad6130a001245..6fb8ea642ba26510126f59066303db015fb9b068 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 35f0963e83214b7b5bf80935aacd5c13317ca17a..0aef194252c0869850973bbd2bd5a707c59b7bf7 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
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'
}
}
}
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 35f0963e83214b7b5bf80935aacd5c13317ca17a..0aef194252c0869850973bbd2bd5a707c59b7bf7 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/cutadapt/2.1/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 75f8575f7a22b66f97bf90241244491cf3dc22f6..30b3b0f9aa96bfa2da9e599de557728a79ced0f5 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -55,28 +55,30 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
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'
}
}
process{
withName: bam_to_bigwig {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index f20b5a82a9af4b7bbcb60bcbbb47f2ec1489a71e..bb3d987f6e5a9426e8e107a75d5feaf422836399 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: compute_matrix {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
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'
}
}
}
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index d31d37abbc9feca96d1cafaf1dd76fdaef6c60bf..de2276e87df8ca0aab46228dddcd8da1895aa2ea 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: plot_profile {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/deeptools/3.0.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 93ebee835ba363c622e55fc7071832362395f545..b93eccd12c12f174544572e18bfc37a8d7267515 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastp/0.19.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
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'
}
}
}
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 93ebee835ba363c622e55fc7071832362395f545..b93eccd12c12f174544572e18bfc37a8d7267515 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastp/0.19.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index e6404b8ff41d9520e0f5e4a85f39e77e8ac2bfa4..a74fb9516fd5f2ea8bfc37224e6a517f38443320 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
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'
}
}
}
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index e6404b8ff41d9520e0f5e4a85f39e77e8ac2bfa4..a74fb9516fd5f2ea8bfc37224e6a517f38443320 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 3292c31618ded91b901a0d7da487f1e21554b9d8..c56f181926f4635130604382bf0b1f28003c8b80 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
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'
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 3def29115ca1faa18c91420a32eed2d7acd6ae36..23a4acc52afd87c3833e0e5afd00e3fe20d0837b 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 3def29115ca1faa18c91420a32eed2d7acd6ae36..23a4acc52afd87c3833e0e5afd00e3fe20d0837b 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/hisat2/2.1.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
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'
}
}
}
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index f3667f4f02d72675487ae9d4d73fab337110b53a..ec072e0bde47065fa0ae78037b63e7eeb448dc8e 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -34,7 +34,7 @@ profiles {
time = "12h"
queue = 'monointeldeb128'
}
- withName: trimming {
+ withName: counting {
beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
module = "htseq/0.11.2"
executor = "sge"
@@ -49,26 +49,28 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
- withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/htseq/0.11.2/:/usr/bin:$PATH"
+ withName: counting {
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/htseq_0.11.2"
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'
}
}
}
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index b51369e15222c19f5ae02e8641d51d8fa18fc538..501daa09be882548eb97d3c184bf846ea7391e0b 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -34,20 +34,6 @@ profiles {
}
}
ccin2p3 {
- process{
- withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
- scratch = true
- stageInMode = "copy"
- stageOutMode = "rsync"
- executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
- cpus = 1
- queue = 'huge'
- }
- }
- }
- ccin2p3_conda {
process{
withName: index_fasta {
beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
@@ -57,7 +43,7 @@ profiles {
stageOutMode = "rsync"
executor = "sge"
clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
- -o /sps/lbmc/lmodolo/logs/ -e /sps/lbmc/lmodolo/logs/"
+ -o ~/logs/ -e ~/logs/"
cpus = 1
queue = 'huge'
}
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 48ee3405404c76f2f94f0f9a9f5d25ece351cd4b..bfbbb6b212a00b0f9bf1027788413c556a3ba0b8 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
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'
}
}
}
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 48ee3405404c76f2f94f0f9a9f5d25ece351cd4b..bfbbb6b212a00b0f9bf1027788413c556a3ba0b8 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/kallisto/0.44.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 2eaed2e7160d91380c5ad08d18ec027c60338fdf..3538315e7c06c9264767a1338b81289f81b29ddd 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -35,16 +35,17 @@ profiles {
}
ccin2p3 {
process{
- withName: peak_calling {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/macs2/2.1.2/:/usr/bin:$PATH"
+ withName: mapping_fastq {
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/macs2_2.1.2"
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'
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 3824f623bda22d752b95941e18acce0eec0b2dbc..51afdbb3b83fd3df10e211b3943da1d87b8bfd36 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -58,26 +58,28 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
withName: multiqc {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/multiqc/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
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'
}
}
}
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index b451a30c2cc2882febc64cd5fcaf2bfb25cacde1..bde67e34b78428677e741dbe1bcf4e5e99bc572d 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -57,26 +57,28 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/fastqc/0.11.5/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
withName: multiqc {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/multiqc/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
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'
}
}
}
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index 1ae50627b88fa356b6df2ad885c3b90b185284aa..bd7036b02964a8a0f6fe16c38e6d4e623d33c9f8 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -104,5 +104,43 @@ profiles {
time = "24h"
}
}
+ process{
+ withName: compute_mappability {
+ beforeScript = "sh /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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: music_preprocessing {
+ beforeScript = "sh /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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ withName: music_computation {
+ beforeScript = "sh /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/"
+ cpus = 1
+ queue = 'huge'
+ }
+ }
}
}
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index a85d7233c6ea571a0b0488e256aa864a4153c521..03ee920b70c9ce57701c6c776816be5901604415 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 58baa5c68550068751be70a555ce58f2cdd5dfeb..4f859c2e700d4a8a75b5d115f3482f98601bea02 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
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'
}
}
}
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 58baa5c68550068751be70a555ce58f2cdd5dfeb..4f859c2e700d4a8a75b5d115f3482f98601bea02 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/rsem/1.3.0/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index dd88348a0aa63f72a3f3c08e7cdc2472596fa9f6..335f0fa65a67dda8bc81b45a02c9ff019fe83b65 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
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'
}
}
}
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index fe605cf4bc9ed80cf1a0abe0b18d2da8a6b90579..6865c9a3a55d04ce5fce5bee68d9313702a4b84c 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 087a0dd57e9c1135483332e4e728eebdd806e799..740c51e001c652cbd4eacb4c12181e82ffbb474e 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sambamba/0.6.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
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'
}
}
}
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 883cbe69e2e1707c8e003b1132b98e7852bcdcac..951d6f87877131c66623699e65575c6f9a1b9243 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: dedup_sam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samblaster/0.1.24/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samblaster_0.1.24"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index c8bab8dbf6c4a45d29029dbe8975a25f46757b6d..f2f899b67ae6a34b6e303bd3f1ded7b98721d8e3 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: filter_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
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'
}
}
}
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 89c223b4f0a6a694c7257f58d5de867f9043bc8e..d5336bb05f64d806d6e165343682b14b3e8c563c 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 6d30cc5bdff88ab781705274c24a1b986867bfdc..8d1153d249c06519d267e4b6efd568f3f26c7866 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
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'
}
}
}
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 9cd8b166eb4038b57d25fb42faa28cc80711537f..7250173170413da238b64a89364d3548c12e9900 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/samtools/1.7/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 8c1087e5c70b88a928e4aab91b467b9def73a202..664482e0908655bd77ecd76407d277d1a71b6235 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -35,15 +35,16 @@ profiles {
ccin2p3 {
process{
withName: fastq_dump {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/sratoolkit/2.8.2/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/sratoolkit_2.8.2"
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'
}
}
}
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 32ccee843f4a794f302f39dccbb5c093c435d3cd..1b250b3967f4e1bd657a6880841691032a458a91 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/urqt/d62c1f8/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
scratch = true
stageInMode = "copy"
stageOutMode = "rsync"
executor = "sge"
- clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n"
+ clusterOptions = "-P P_lbmc -l os=cl7 -l sps=1 -r n \
+ -o ~/logs/ -e ~/logs/"
cpus = 1
- memory = "10GB"
- time = "24h"
+ queue = 'huge'
}
}
}
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index d4c9b3ac8a6c459f550998d8143607cb7db00753..b107cf2271706a4e66c65b0ed5a8c53a8f74a650 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -36,15 +36,16 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "PATH=/sps/lbmc/common/nextflow/src/singularity_modules/urqt/d62c1f8/:/usr/bin:$PATH"
+ beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
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'
}
}
}