diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index d8dc120c93daae9550844ce32526a212006a5e3a..3372d4521d17985fb4ca728471c2a9df7d81c5d6 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fasta_from_bed {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 05d5c9412e598d26bbed994eb06caf50c81220d5..32db140ee33a72bbb2a158fa095d2086ecc98ef7 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_fasta {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 545ba4d4329d867fa5e451e616eaa433c5cd800b..4aa916d048cd584ce581da5d10c83f48b54b7dc6 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 545ba4d4329d867fa5e451e616eaa433c5cd800b..4aa916d048cd584ce581da5d10c83f48b54b7dc6 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 6e9cef00c89357a072bfaf3e4e391b14e611c12a..0fcb85076d45b52eec1eec594dce9cc761cdce52 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_fasta {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 48ba0b18e35f533be0843c7b37f93b0f7d570d18..7111d23964d7a395cb3073f8611ece22d7416dd5 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 48ba0b18e35f533be0843c7b37f93b0f7d570d18..7111d23964d7a395cb3073f8611ece22d7416dd5 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index adee7793a98da076def5454b020a933204084d33..b852e1535a55ce2cd0d7f4ae71a1d3b7bd91239e 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_fasta {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 815292498a00be5f91cd62a8b430a29a3cca1f8e..b493b5f4588f560242e4e426a3644115ae98169e 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 79818d9554cd58c09781d90345dc11e0cc7893b9..c6ad6528b06f0bf6ceb49fd10a7eacf0e0fed3e9 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: adaptor_removal {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 79818d9554cd58c09781d90345dc11e0cc7893b9..c6ad6528b06f0bf6ceb49fd10a7eacf0e0fed3e9 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: adaptor_removal {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 30faba103bd22a2a7682d476dd677f3e8caab5d0..edbee7135ba417a1fbf22994218f8651e16f9874 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -33,21 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: trimming {
- beforeScript = "source /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"
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 30faba103bd22a2a7682d476dd677f3e8caab5d0..edbee7135ba417a1fbf22994218f8651e16f9874 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -33,21 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: trimming {
- beforeScript = "source /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"
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index ffb6271143ccbe15f04676f7cd487315e27cb469..a30225b8e9cb3d182f269357737ee6bba6d0eda6 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -53,34 +53,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_bam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- withName: bam_to_bigwig {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index f6c49a3a7270d6790289c8841717f3b31af0faf6..2e1780448189a6a6ec77bd014b33bb8372775c41 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: compute_matrix {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 99ea5acb051a86a1913f0c885d45e6d2f4cf6f3b..cceb474689ad337c7aadae57c1df243ff569c407 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: plot_profile {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index b7e89b3463a900812c1b316f6c1069ebb03f5cac..a9129ddb4cad6b229a9f4b22d68bb38f34b061b6 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fastp_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index b7e89b3463a900812c1b316f6c1069ebb03f5cac..a9129ddb4cad6b229a9f4b22d68bb38f34b061b6 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fastp_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index c0db2aa86a709df9e252680dfd82cc2b8ca71653..e01fa5f52068fad45dd556d65cd4504286025a9a 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fastqc_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index c0db2aa86a709df9e252680dfd82cc2b8ca71653..e01fa5f52068fad45dd556d65cd4504286025a9a 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fastqc_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 443c33aff182cc21dbdb70e39b36f39aaf177217..6322661b25edef46879c2256dc639ea0dec3fdcc 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_fasta {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index e0d73fc288afc9d5875210ea52a7f949d4713880..860fc2f72d6f9fed0e1168814ba64401d36e82ff 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index e0d73fc288afc9d5875210ea52a7f949d4713880..860fc2f72d6f9fed0e1168814ba64401d36e82ff 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 4840d58a87d93bf80149aa699276040a44f5d36f..52c8ae869faec9ebaa5675f6dfe79c35f32d2b20 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -51,34 +51,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: sort_bam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- withName: counting {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index fefa4c335fb4a9d3463b425a982a2b8cb886aef5..9bbba3d67f9171848350afbb02bf855e63ba2033 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_fasta {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index dc990d3a929ccc3f6c538f5380efdeb59305e25e..5e1784b9f7ce4b2a4f28e4b9d311430a8813f3d0 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index dc990d3a929ccc3f6c538f5380efdeb59305e25e..5e1784b9f7ce4b2a4f28e4b9d311430a8813f3d0 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 5122f5f65aecef415fb032e18a423554c0128d43..747f26bb94aa8f07b0b8e4c3154de725c6522a3b 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index e5329fc8435955b634573effa930e861f9b51301..0b220310b684e2a7ce6eb78fe537eafc34791bc4 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -56,34 +56,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fastqc_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- withName: multiqc {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index d7239b9e4f0825163246cee3746a276fd608424a..80ecd7fd72ce8c159c8454a4b6d2acf0e490bebc 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -55,34 +55,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fastqc_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- withName: multiqc {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index e14192e5d95f56061551e558e2dc8e3361fa4519..012619074e0a3ab718fa15b1e25b07e22f170a63 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -69,46 +69,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: compute_mappability {
- 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\
- "
- cpus = 1
- queue = 'huge'
- }
- withName: music_preprocessing {
- 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\
- "
- 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"
- 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 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 851d0cfbf1a8a08bc5476fc74f6b608eb8d330c9..be6169e26c8191dbf0bf173817e2ed53d2aa185a 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_fasta {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index a0589cb6578aab5b45588d73ed258bc5e1f1a73b..97502ecda4b3590a0f35103e29806e5ec7adf9e2 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index a0589cb6578aab5b45588d73ed258bc5e1f1a73b..97502ecda4b3590a0f35103e29806e5ec7adf9e2 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: mapping_fastq {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index d144dcb3a265718e75f9283eb253b7f5ede7b636..95cb2371b0b0a1f77fb8b6fe6acd75e5a5c2ea52 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_bam {
- beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
- 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 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 896fb342542613f41bfd87628ed193dc3117606b..3dd3273b48a005fcf0ccce3c49d2dc669de69e42 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: sort_bam {
- beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
- 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 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 967a79a30a784fdcd4099c676d285f3dff776c36..c774bd7fcbe53b7eabb4ec6205fad92655aeed1f 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: split_bam {
- beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
- 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 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 6dab50bcdf7e2b27371df68103761dff07d3b98c..cd17da0112b93c8cde720ef0c80efd8710020ce2 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: dedup_sam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 9d7dbe0f8c978cdf1a280c6be6e726d210123fb9..a909fd16e8bc23b7a2b12555611128cf84d4c82b 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: filter_bam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 765e75e84d6fc26319c8a38ac41dba07dfb76263..1ab10017eff019dfcb0d150c00cb608a914a8015 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: index_bam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index f2b401c10a9e0884c58f7e53ce98d07d1c912c86..d3bbfa8b8850676c2bc310c6e5e2621215646a3c 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: sort_bam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 0462310f9fc9816ca4ee4b8195dfe4d172418f70..56b1eafcd783d120f876468c04efba275f933cd8 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: split_bam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 924aa0d285d4d954cb3129a30e23ff422fb36364..e01b71bc8cab55e79ca05dcf5b371c9a81653840 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -33,22 +33,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: fastq_dump {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 31675091b31d8f1cb047d92e79e38481b294f3a2..f0153ffadb04419b9ac1d296a7b975a1649a1316 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -51,34 +51,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: sort_bam {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- withName: counting {
- beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
- conda = "/sps/lbmc/common/miniconda3/envs/subread_1.6.4"
- 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 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index e5e61dbdd59060daaac86032cbd8b106dfa9c905..4d8b855f120edce826f4306c97d6d23f768189e2 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: trimming {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index f70917233c63134405d52c0a10a796b3b8dc9ca9..b8b8fc16153f2b99c61a69ffd7a550fdd4835972 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -34,22 +34,6 @@ profiles {
}
}
}
- ccin2p3_conda {
- process{
- withName: trimming {
- beforeScript = "source /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\
- "
- cpus = 1
- queue = 'huge'
- }
- }
- }
ccin2p3 {
singularity.enabled = true
singularity.cacheDir = "/sps/lbmc/common/singularity/"