From cbe801289896617f1d14cef12a013fd78ad10f30 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 13 Nov 2019 17:51:48 +0100
Subject: [PATCH] nf_modules: rm ccin2p3_conda section in config files
---
src/nf_modules/bedtools/fasta_from_bed.config | 16 --------
src/nf_modules/bowtie/indexing.config | 16 --------
src/nf_modules/bowtie/mapping_paired.config | 16 --------
src/nf_modules/bowtie/mapping_single.config | 16 --------
src/nf_modules/bowtie2/indexing.config | 16 --------
src/nf_modules/bowtie2/mapping_paired.config | 16 --------
src/nf_modules/bowtie2/mapping_single.config | 16 --------
src/nf_modules/bwa/indexing.config | 16 --------
src/nf_modules/bwa/mapping_paired.config | 16 --------
.../cutadapt/adaptor_removal_paired.config | 16 --------
.../cutadapt/adaptor_removal_single.config | 16 --------
.../cutadapt/trimming_paired.config | 15 -------
.../cutadapt/trimming_single.config | 15 -------
src/nf_modules/deeptools/bam_to_bigwig.config | 28 -------------
.../deeptools/compute_matrix.config | 16 --------
src/nf_modules/deeptools/plot_profile.config | 16 --------
src/nf_modules/fastp/fastp_paired.config | 16 --------
src/nf_modules/fastp/fastp_single.config | 16 --------
src/nf_modules/fastqc/fastqc_paired.config | 16 --------
src/nf_modules/fastqc/fastqc_single.config | 16 --------
src/nf_modules/hisat2/indexing.config | 16 --------
src/nf_modules/hisat2/mapping_paired.config | 16 --------
src/nf_modules/hisat2/mapping_single.config | 16 --------
src/nf_modules/htseq/htseq.config | 28 -------------
src/nf_modules/kallisto/indexing.config | 16 --------
src/nf_modules/kallisto/mapping_paired.config | 16 --------
src/nf_modules/kallisto/mapping_single.config | 16 --------
src/nf_modules/macs2/peak_calling.config | 16 --------
src/nf_modules/multiqc/multiqc_paired.config | 28 -------------
src/nf_modules/multiqc/multiqc_single.config | 28 -------------
.../music/peak_calling_single.config | 40 -------------------
src/nf_modules/rsem/indexing.config | 16 --------
.../rsem/quantification_paired.config | 16 --------
.../rsem/quantification_single.config | 16 --------
src/nf_modules/sambamba/index_bams.config | 16 --------
src/nf_modules/sambamba/sort_bams.config | 16 --------
src/nf_modules/sambamba/split_bams.config | 16 --------
src/nf_modules/samblaster/dedup_sams.config | 16 --------
src/nf_modules/samtools/filter_bams.config | 16 --------
src/nf_modules/samtools/index_bams.config | 16 --------
src/nf_modules/samtools/sort_bams.config | 16 --------
src/nf_modules/samtools/split_bams.config | 16 --------
src/nf_modules/sratoolkit/fastqdump.config | 16 --------
src/nf_modules/subread/subread.config | 28 -------------
src/nf_modules/urqt/trimming_paired.config | 16 --------
src/nf_modules/urqt/trimming_single.config | 16 --------
46 files changed, 818 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index d8dc120..3372d45 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 05d5c94..32db140 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 545ba4d..4aa916d 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 545ba4d..4aa916d 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 6e9cef0..0fcb850 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 48ba0b1..7111d23 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 48ba0b1..7111d23 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 adee779..b852e15 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 8152924..b493b5f 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 79818d9..c6ad652 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 79818d9..c6ad652 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 30faba1..edbee71 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 30faba1..edbee71 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 ffb6271..a30225b 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 f6c49a3..2e17804 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 99ea5ac..cceb474 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 b7e89b3..a9129dd 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 b7e89b3..a9129dd 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 c0db2aa..e01fa5f 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 c0db2aa..e01fa5f 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 443c33a..6322661 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 e0d73fc..860fc2f 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 e0d73fc..860fc2f 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 4840d58..52c8ae8 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 fefa4c3..9bbba3d 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 dc990d3..5e1784b 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 dc990d3..5e1784b 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 5122f5f..747f26b 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 e5329fc..0b22031 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 d7239b9..80ecd7f 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 e14192e..0126190 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 851d0cf..be6169e 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 a0589cb..97502ec 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 a0589cb..97502ec 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 d144dcb..95cb237 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 896fb34..3dd3273 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 967a79a..c774bd7 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 6dab50b..cd17da0 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 9d7dbe0..a909fd1 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 765e75e..1ab1001 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 f2b401c..d3bbfa8 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 0462310..56b1eaf 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 924aa0d..e01b71b 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 3167509..f0153ff 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 e5e61db..4d8b855 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 f709172..b8b8fc1 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/"
--
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