From b43a5a48cb953afedc1db582b2812fd8003a9cfb Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent@modolo.fr>
Date: Wed, 6 Nov 2019 18:05:06 +0100
Subject: [PATCH] conda_psmn: fix path of the scripts in configs files
---
src/nf_modules/bedtools/fasta_from_bed.config | 4 ++--
src/nf_modules/bowtie/indexing.config | 4 ++--
src/nf_modules/bowtie/mapping_paired.config | 4 ++--
src/nf_modules/bowtie/mapping_single.config | 4 ++--
src/nf_modules/bowtie2/indexing.config | 4 ++--
src/nf_modules/bowtie2/mapping_paired.config | 4 ++--
src/nf_modules/bowtie2/mapping_single.config | 4 ++--
src/nf_modules/bwa/indexing.config | 4 ++--
src/nf_modules/bwa/mapping_paired.config | 4 ++--
.../cutadapt/adaptor_removal_paired.config | 4 ++--
.../cutadapt/adaptor_removal_single.config | 4 ++--
.../cutadapt/trimming_paired.config | 4 ++--
.../cutadapt/trimming_single.config | 4 ++--
src/nf_modules/deeptools/bam_to_bigwig.config | 4 ++--
.../deeptools/compute_matrix.config | 4 ++--
src/nf_modules/deeptools/plot_profile.config | 4 ++--
src/nf_modules/fastp/fastp_paired.config | 4 ++--
src/nf_modules/fastp/fastp_single.config | 4 ++--
src/nf_modules/fastqc/fastqc_paired.config | 4 ++--
src/nf_modules/fastqc/fastqc_single.config | 4 ++--
src/nf_modules/hisat2/indexing.config | 4 ++--
src/nf_modules/htseq/htseq.config | 4 ++--
src/nf_modules/kallisto/indexing.config | 4 ++--
src/nf_modules/kallisto/mapping_paired.config | 4 ++--
src/nf_modules/kallisto/mapping_single.config | 4 ++--
src/nf_modules/macs2/peak_calling.config | 4 ++--
src/nf_modules/multiqc/multiqc_paired.config | 4 ++--
src/nf_modules/multiqc/multiqc_single.config | 4 ++--
.../music/peak_calling_single.config | 4 ++--
src/nf_modules/rsem/indexing.config | 4 ++--
.../rsem/quantification_paired.config | 4 ++--
.../rsem/quantification_single.config | 4 ++--
src/nf_modules/sambamba/index_bams.config | 4 ++--
src/nf_modules/sambamba/sort_bams.config | 4 ++--
src/nf_modules/sambamba/split_bams.config | 4 ++--
src/nf_modules/samblaster/dedup_sams.config | 4 ++--
src/nf_modules/samtools/filter_bams.config | 4 ++--
src/nf_modules/samtools/index_bams.config | 4 ++--
src/nf_modules/samtools/sort_bams.config | 4 ++--
src/nf_modules/samtools/split_bams.config | 4 ++--
src/nf_modules/sratoolkit/fastqdump.config | 4 ++--
src/nf_modules/subread/subread.config | 4 ++--
src/nf_modules/urqt/trimming_paired.config | 4 ++--
src/nf_modules/urqt/trimming_single.config | 4 ++--
src/training_dataset.config | 22 +++++++++----------
45 files changed, 99 insertions(+), 99 deletions(-)
diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 574e6d73..d8dc120c 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fasta_from_bed {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bedtools_2.25.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/${CONDA_ENVS}bedtools_2.25.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 4b554a7b..05d5c941 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bowtie_1.2.2"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie_1.2.2"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 49eb9c53..99723a35 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bowtie/1.2.2:samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie/1.2.2:samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 49eb9c53..99723a35 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bowtie/1.2.2:samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie/1.2.2:samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 5ed9bcc3..6e9cef00 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bowtie2_2.3.4.1"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index bc1c8979..48ba0b18 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bowtie2_2.3.4.1"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index bc1c8979..48ba0b18 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bowtie2_2.3.4.1"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index 4e89c3be..adee7793 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bwa_0.7.17"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index aebe28c5..81529249 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "bwa_0.7.17"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/bwa_0.7.17"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 8e62c1cc..79818d95 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: adaptor_removal {
- beforeScript = "./src/conda_psmn.sh"
- conda = "cutadapt_2.1"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 8e62c1cc..79818d95 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: adaptor_removal {
- beforeScript = "./src/conda_psmn.sh"
- conda = "cutadapt_2.1"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index f94b4e48..30faba10 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "./src/conda_psmn.sh"
- conda = "cutadapt_2.1"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index f94b4e48..30faba10 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "./src/conda_psmn.sh"
- conda = "cutadapt_2.1"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/cutadapt_2.1"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 13952d87..ffb62711 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -30,8 +30,8 @@ profiles {
psmn{
process{
withName: index_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "sambamba_0.6.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/sambamba_0.6.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index ea4bab25..f6c49a3a 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: compute_matrix {
- beforeScript = "./src/conda_psmn.sh"
- conda = "deeptools_3.0.2"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index 18483547..99ea5acb 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: plot_profile {
- beforeScript = "./src/conda_psmn.sh"
- conda = "deeptools_3.0.2"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/deeptools_3.0.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index 6cece587..b7e89b34 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastp_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "fastp_0.19.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/fastp_0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index 6cece587..b7e89b34 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastp_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "fastp_0.19.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/fastp_0.19.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index 6731be65..c0db2aa8 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "fastqc_0.11.5"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index 6731be65..c0db2aa8 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "fastqc_0.11.5"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index 01646ee1..443c33af 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "./src/conda_psmn.sh"
- conda = "hisat2_2.1.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/hisat2_2.1.0"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "20GB"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index 8d1d4472..4840d58a 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -30,8 +30,8 @@ profiles {
psmn{
process{
withName: sort_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 8a038dd9..fefa4c33 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "./src/conda_psmn.sh"
- conda = "kallisto_0.44.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index 8ac5af00..dc990d3a 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "kallisto_0.44.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index 8ac5af00..dc990d3a 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "kallisto_0.44.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/kallisto_0.44.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index d9a72019..5122f5f6 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: peak_calling {
- beforeScript = "./src/conda_psmn.sh"
- conda = "macs2_2.1.2"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/macs2_2.1.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 40754658..e5329fc8 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -31,8 +31,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "fastqc_0.11.5"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index f440d146..d7239b9e 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -30,8 +30,8 @@ profiles {
psmn{
process{
withName: fastqc_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "fastqc_0.11.5"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/fastqc_0.11.5"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index d0841719..e14192e5 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -38,8 +38,8 @@ profiles {
psmn{
process{
withName: compute_mappability {
- beforeScript = "./src/conda_psmn.sh"
- conda = "music_6613c53"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/music_6613c53"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index d49f444a..851d0cfb 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_fasta {
- beforeScript = "./src/conda_psmn.sh"
- conda = "rsem_1.3.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 90eaae70..a0589cb6 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "rsem_1.3.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 90eaae70..a0589cb6 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: mapping_fastq {
- beforeScript = "./src/conda_psmn.sh"
- conda = "rsem_1.3.0"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/rsem_1.3.0"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index d1dd2c3a..d144dcb3 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "sambamba_0.6.9"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index 145fa48d..896fb342 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: sort_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "sambamba_0.6.9"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 4
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index afd305f9..967a79a3 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: split_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "sambamba_0.6.9"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/sambamba_0.6.9"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 0b4f093b..6dab50bc 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: dedup_sam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "samblaster_0.1.24"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samblaster_0.1.24"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index 69f9664f..9d7dbe0f 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: filter_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index 49bc53f8..765e75e8 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: index_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 8436342a..f2b401c1 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: sort_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index eb4468d9..0462310f 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: split_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index ad33eec9..924aa0d2 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: fastq_dump {
- beforeScript = "./src/conda_psmn.sh"
- conda = "sratoolkit_2.8.2"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/sratoolkit_2.8.2"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/subread/subread.config b/src/nf_modules/subread/subread.config
index 4e8e0340..31675091 100644
--- a/src/nf_modules/subread/subread.config
+++ b/src/nf_modules/subread/subread.config
@@ -30,8 +30,8 @@ profiles {
psmn{
process{
withName: sort_bam {
- beforeScript = "./src/conda_psmn.sh"
- conda = "samtools_1.7"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 1
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index ccc10311..e5e61dbd 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "./src/conda_psmn.sh"
- conda = "urqt_d62c1f8"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/urqt_d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
memory = "5GB"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index a9806ceb..f7091723 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -22,8 +22,8 @@ profiles {
psmn{
process{
withName: trimming {
- beforeScript = "./src/conda_psmn.sh"
- conda = "urqt_d62c1f8"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
+ conda = "$baseDir/.conda_envs/urqt_d62c1f8"
executor = "sge"
clusterOptions = "-cwd -V"
cpus = 16
diff --git a/src/training_dataset.config b/src/training_dataset.config
index deb62fec..453e7b7e 100644
--- a/src/training_dataset.config
+++ b/src/training_dataset.config
@@ -118,7 +118,7 @@ profiles {
psmn {
process{
withName: build_synthetic_bed {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -128,7 +128,7 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: fasta_from_bed {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bedtools_2.25.0"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -138,7 +138,7 @@ profiles {
queue = 'monointeldeb128,monointeldeb48,h48-E5-2670deb128,h6-E5-2667v4deb128'
}
withName: index_fasta {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -149,7 +149,7 @@ profiles {
penv = 'openmp16'
}
withName: mapping_fastq_paired {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -160,7 +160,7 @@ profiles {
penv = 'openmp16'
}
withName: bam_2_fastq_paired {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -171,7 +171,7 @@ profiles {
penv = 'openmp16'
}
withName: sort_bam_paired {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -182,7 +182,7 @@ profiles {
penv = 'openmp16'
}
withName: index_bam_paired {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -193,7 +193,7 @@ profiles {
penv = 'openmp16'
}
withName: mapping_fastq_single {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/bowtie2_2.3.4.1"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -204,7 +204,7 @@ profiles {
penv = 'openmp16'
}
withName: bam_2_fastq_single {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -215,7 +215,7 @@ profiles {
penv = 'openmp16'
}
withName: sort_bam_single {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
@@ -226,7 +226,7 @@ profiles {
penv = 'openmp16'
}
withName: index_bam_single {
- beforeScript = "source $baseDir/conda_psmn.sh"
+ beforeScript = "source $baseDir/.conda_psmn.sh"
conda = "$baseDir/.conda_envs/samtools_1.7"
executor = "sge"
clusterOptions = "-m e -cwd -V"
--
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