diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 17dee4b14b8ad9e56706506d0351ca31324c0052..7a2e982b600288fe8dcb31e588b663adc3533b44 100644
--- a/src/nf_modules/bedtools/fasta_from_bed.config
+++ b/src/nf_modules/bedtools/fasta_from_bed.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fasta_from_bed {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bedtools_2.25.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/indexing.config b/src/nf_modules/bowtie/indexing.config
index 627cc943b698862f28c2182673d311958726902a..0f6fd4940eba2805ae84b179be0eef0a6d98d62b 100644
--- a/src/nf_modules/bowtie/indexing.config
+++ b/src/nf_modules/bowtie/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/mapping_paired.config b/src/nf_modules/bowtie/mapping_paired.config
index 598b99a1706fa751c2fe6cec668ec08b192ac2b5..3582d00fdea05fc904399732ed01bfea3fee35b2 100644
--- a/src/nf_modules/bowtie/mapping_paired.config
+++ b/src/nf_modules/bowtie/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie/mapping_single.config b/src/nf_modules/bowtie/mapping_single.config
index 598b99a1706fa751c2fe6cec668ec08b192ac2b5..3582d00fdea05fc904399732ed01bfea3fee35b2 100644
--- a/src/nf_modules/bowtie/mapping_single.config
+++ b/src/nf_modules/bowtie/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie_1.2.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/indexing.config b/src/nf_modules/bowtie2/indexing.config
index 966b7a9f9a238627809c670e1d00c02226e65d97..85480186a10df0359ed0af25d5d85aedc8a2aff1 100644
--- a/src/nf_modules/bowtie2/indexing.config
+++ b/src/nf_modules/bowtie2/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/mapping_paired.config b/src/nf_modules/bowtie2/mapping_paired.config
index 5c975a8c7d2405745546477466b99b134df3b3cf..3584a222226e410d0177118283e97a32e185989e 100644
--- a/src/nf_modules/bowtie2/mapping_paired.config
+++ b/src/nf_modules/bowtie2/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bowtie2/mapping_single.config b/src/nf_modules/bowtie2/mapping_single.config
index 5c975a8c7d2405745546477466b99b134df3b3cf..3584a222226e410d0177118283e97a32e185989e 100644
--- a/src/nf_modules/bowtie2/mapping_single.config
+++ b/src/nf_modules/bowtie2/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bowtie2_2.3.4.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bwa/indexing.config b/src/nf_modules/bwa/indexing.config
index eeb59fad260a079e53e9d882fecfbf3aba4c9707..4fcea110abcf27428b4852cd9c592b87db835bb9 100644
--- a/src/nf_modules/bwa/indexing.config
+++ b/src/nf_modules/bwa/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/bwa/mapping_paired.config b/src/nf_modules/bwa/mapping_paired.config
index 7b96412036b71dd7aaa115fda671b55317ffede6..d1f05908884afc7fae2e665a90bd0cb7c5f7d06a 100644
--- a/src/nf_modules/bwa/mapping_paired.config
+++ b/src/nf_modules/bwa/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/bwa_0.7.17"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_paired.config b/src/nf_modules/cutadapt/adaptor_removal_paired.config
index 6fb8ea642ba26510126f59066303db015fb9b068..b635d8a89d3a4aca02eba25d81bfa45f3543896f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_paired.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/adaptor_removal_single.config b/src/nf_modules/cutadapt/adaptor_removal_single.config
index 6fb8ea642ba26510126f59066303db015fb9b068..b635d8a89d3a4aca02eba25d81bfa45f3543896f 100644
--- a/src/nf_modules/cutadapt/adaptor_removal_single.config
+++ b/src/nf_modules/cutadapt/adaptor_removal_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: adaptor_removal {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/trimming_paired.config b/src/nf_modules/cutadapt/trimming_paired.config
index 0aef194252c0869850973bbd2bd5a707c59b7bf7..3ebf0514832103f0d584a63715001dbd5c82efda 100644
--- a/src/nf_modules/cutadapt/trimming_paired.config
+++ b/src/nf_modules/cutadapt/trimming_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/cutadapt/trimming_single.config b/src/nf_modules/cutadapt/trimming_single.config
index 0aef194252c0869850973bbd2bd5a707c59b7bf7..3ebf0514832103f0d584a63715001dbd5c82efda 100644
--- a/src/nf_modules/cutadapt/trimming_single.config
+++ b/src/nf_modules/cutadapt/trimming_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/cutadapt_2.1"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/deeptools/bam_to_bigwig.config b/src/nf_modules/deeptools/bam_to_bigwig.config
index 30b3b0f9aa96bfa2da9e599de557728a79ced0f5..bf1ebd09c46d0472cfa59f2f74f9da031c91a90d 100644
--- a/src/nf_modules/deeptools/bam_to_bigwig.config
+++ b/src/nf_modules/deeptools/bam_to_bigwig.config
@@ -55,7 +55,7 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.7"
scratch = true
stageInMode = "copy"
@@ -69,7 +69,7 @@ profiles {
}
process{
withName: bam_to_bigwig {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/deeptools/compute_matrix.config b/src/nf_modules/deeptools/compute_matrix.config
index bb3d987f6e5a9426e8e107a75d5feaf422836399..76ccaa7a802aab4a742b3d836b7e210f401b510f 100644
--- a/src/nf_modules/deeptools/compute_matrix.config
+++ b/src/nf_modules/deeptools/compute_matrix.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: compute_matrix {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/deeptools/plot_profile.config b/src/nf_modules/deeptools/plot_profile.config
index de2276e87df8ca0aab46228dddcd8da1895aa2ea..eca7b8bbf2e135f8d043459756105e5a410599d1 100644
--- a/src/nf_modules/deeptools/plot_profile.config
+++ b/src/nf_modules/deeptools/plot_profile.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: plot_profile {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/deeptools_3.0.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastp/fastp_paired.config b/src/nf_modules/fastp/fastp_paired.config
index b93eccd12c12f174544572e18bfc37a8d7267515..f4b0d892adeb9d801d8c32f11f8f4015f55cdf42 100644
--- a/src/nf_modules/fastp/fastp_paired.config
+++ b/src/nf_modules/fastp/fastp_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastp/fastp_single.config b/src/nf_modules/fastp/fastp_single.config
index b93eccd12c12f174544572e18bfc37a8d7267515..f4b0d892adeb9d801d8c32f11f8f4015f55cdf42 100644
--- a/src/nf_modules/fastp/fastp_single.config
+++ b/src/nf_modules/fastp/fastp_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastp_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastp_0.19.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastqc/fastqc_paired.config b/src/nf_modules/fastqc/fastqc_paired.config
index a74fb9516fd5f2ea8bfc37224e6a517f38443320..bdeaeac70ee9489e812f6063802d33d8f7d7acbd 100644
--- a/src/nf_modules/fastqc/fastqc_paired.config
+++ b/src/nf_modules/fastqc/fastqc_paired.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/fastqc/fastqc_single.config b/src/nf_modules/fastqc/fastqc_single.config
index a74fb9516fd5f2ea8bfc37224e6a517f38443320..bdeaeac70ee9489e812f6063802d33d8f7d7acbd 100644
--- a/src/nf_modules/fastqc/fastqc_single.config
+++ b/src/nf_modules/fastqc/fastqc_single.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/hisat2/indexing.config b/src/nf_modules/hisat2/indexing.config
index c56f181926f4635130604382bf0b1f28003c8b80..6214ad49ff0d8c441af98541a9d1051099575e3c 100644
--- a/src/nf_modules/hisat2/indexing.config
+++ b/src/nf_modules/hisat2/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/hisat2/mapping_paired.config b/src/nf_modules/hisat2/mapping_paired.config
index 23a4acc52afd87c3833e0e5afd00e3fe20d0837b..95108b57943a09620e63bd3ff2eb0563a236a1c9 100644
--- a/src/nf_modules/hisat2/mapping_paired.config
+++ b/src/nf_modules/hisat2/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/hisat2/mapping_single.config b/src/nf_modules/hisat2/mapping_single.config
index 23a4acc52afd87c3833e0e5afd00e3fe20d0837b..95108b57943a09620e63bd3ff2eb0563a236a1c9 100644
--- a/src/nf_modules/hisat2/mapping_single.config
+++ b/src/nf_modules/hisat2/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/hisat2_2.1.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/htseq/htseq.config b/src/nf_modules/htseq/htseq.config
index ec072e0bde47065fa0ae78037b63e7eeb448dc8e..909056991b56c7087c0e6d7f39531d9e19acdfe1 100644
--- a/src/nf_modules/htseq/htseq.config
+++ b/src/nf_modules/htseq/htseq.config
@@ -49,7 +49,7 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
@@ -61,7 +61,7 @@ profiles {
queue = 'huge'
}
withName: counting {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/htseq_0.11.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/indexing.config b/src/nf_modules/kallisto/indexing.config
index 501daa09be882548eb97d3c184bf846ea7391e0b..a89cc5a37c6f007f71d4e738cf84286ee88f2d1f 100644
--- a/src/nf_modules/kallisto/indexing.config
+++ b/src/nf_modules/kallisto/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_paired.config b/src/nf_modules/kallisto/mapping_paired.config
index bfbbb6b212a00b0f9bf1027788413c556a3ba0b8..f033f789c51747db65d8f34a7e68fe78a89b10fe 100644
--- a/src/nf_modules/kallisto/mapping_paired.config
+++ b/src/nf_modules/kallisto/mapping_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/kallisto/mapping_single.config b/src/nf_modules/kallisto/mapping_single.config
index bfbbb6b212a00b0f9bf1027788413c556a3ba0b8..f033f789c51747db65d8f34a7e68fe78a89b10fe 100644
--- a/src/nf_modules/kallisto/mapping_single.config
+++ b/src/nf_modules/kallisto/mapping_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/kallisto_0.44.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/macs2/peak_calling.config b/src/nf_modules/macs2/peak_calling.config
index 3538315e7c06c9264767a1338b81289f81b29ddd..1670ee68b1c068bd86dd2973635acf2604820be3 100644
--- a/src/nf_modules/macs2/peak_calling.config
+++ b/src/nf_modules/macs2/peak_calling.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/macs2_2.1.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/multiqc/multiqc_paired.config b/src/nf_modules/multiqc/multiqc_paired.config
index 51afdbb3b83fd3df10e211b3943da1d87b8bfd36..71fb79fcfb1a9b3b341b1c8ac311696b62e73e10 100644
--- a/src/nf_modules/multiqc/multiqc_paired.config
+++ b/src/nf_modules/multiqc/multiqc_paired.config
@@ -58,7 +58,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
@@ -70,7 +70,7 @@ profiles {
queue = 'huge'
}
withName: multiqc {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/multiqc/multiqc_single.config b/src/nf_modules/multiqc/multiqc_single.config
index bde67e34b78428677e741dbe1bcf4e5e99bc572d..fdc12e4ee617a7f4d77e1472715bc345cda98edc 100644
--- a/src/nf_modules/multiqc/multiqc_single.config
+++ b/src/nf_modules/multiqc/multiqc_single.config
@@ -57,7 +57,7 @@ profiles {
ccin2p3 {
process{
withName: fastqc_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/fastqc_0.11.5"
scratch = true
stageInMode = "copy"
@@ -69,7 +69,7 @@ profiles {
queue = 'huge'
}
withName: multiqc {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/multiqc_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/music/peak_calling_single.config b/src/nf_modules/music/peak_calling_single.config
index bd7036b02964a8a0f6fe16c38e6d4e623d33c9f8..1dc6900716a52b0b9d49a5ed75b52431df5cd596 100644
--- a/src/nf_modules/music/peak_calling_single.config
+++ b/src/nf_modules/music/peak_calling_single.config
@@ -106,7 +106,7 @@ profiles {
}
process{
withName: compute_mappability {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
@@ -118,7 +118,7 @@ profiles {
queue = 'huge'
}
withName: music_preprocessing {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
@@ -130,7 +130,7 @@ profiles {
queue = 'huge'
}
withName: music_computation {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/music_1.0.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/rsem/indexing.config b/src/nf_modules/rsem/indexing.config
index 03ee920b70c9ce57701c6c776816be5901604415..5747a30f644c419c365e7b39e7edf9484b6f2d8d 100644
--- a/src/nf_modules/rsem/indexing.config
+++ b/src/nf_modules/rsem/indexing.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_fasta {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/rsem/quantification_paired.config b/src/nf_modules/rsem/quantification_paired.config
index 4f859c2e700d4a8a75b5d115f3482f98601bea02..0c1768cce652475d5f0ac91434a95b38de2a805e 100644
--- a/src/nf_modules/rsem/quantification_paired.config
+++ b/src/nf_modules/rsem/quantification_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/rsem/quantification_single.config b/src/nf_modules/rsem/quantification_single.config
index 4f859c2e700d4a8a75b5d115f3482f98601bea02..0c1768cce652475d5f0ac91434a95b38de2a805e 100644
--- a/src/nf_modules/rsem/quantification_single.config
+++ b/src/nf_modules/rsem/quantification_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: mapping_fastq {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/rsem_1.3.0"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sambamba/index_bams.config b/src/nf_modules/sambamba/index_bams.config
index e8ab95accf3973a81f4507b1d6f726efe3036963..818acc4b23a1a084c11adcf90e0787b7d671165b 100644
--- a/src/nf_modules/sambamba/index_bams.config
+++ b/src/nf_modules/sambamba/index_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sambamba/sort_bams.config b/src/nf_modules/sambamba/sort_bams.config
index a408436b56372fc8201978b9dccf231cdd5714b8..c4f8ed2d874e48ba8a4e2ddd6d07c3ccd7a96527 100644
--- a/src/nf_modules/sambamba/sort_bams.config
+++ b/src/nf_modules/sambamba/sort_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sambamba/split_bams.config b/src/nf_modules/sambamba/split_bams.config
index 4bc3cda1036bfe310dc516fc999784a10c6bf4fe..1a7f7bbbf04fdcb3a121d8ffea87ed118f7eba8b 100644
--- a/src/nf_modules/sambamba/split_bams.config
+++ b/src/nf_modules/sambamba/split_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sambamba_0.6.9"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samblaster/dedup_sams.config b/src/nf_modules/samblaster/dedup_sams.config
index 951d6f87877131c66623699e65575c6f9a1b9243..5f00a51e0c926723f2c13f9b884df673e7722815 100644
--- a/src/nf_modules/samblaster/dedup_sams.config
+++ b/src/nf_modules/samblaster/dedup_sams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: dedup_sam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samblaster_0.1.24"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/filter_bams.config b/src/nf_modules/samtools/filter_bams.config
index f2f899b67ae6a34b6e303bd3f1ded7b98721d8e3..65d6c697540a8d1ae6729a844a4fb27d5fddafb8 100644
--- a/src/nf_modules/samtools/filter_bams.config
+++ b/src/nf_modules/samtools/filter_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: filter_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/index_bams.config b/src/nf_modules/samtools/index_bams.config
index d5336bb05f64d806d6e165343682b14b3e8c563c..f47469c1e1249bc48f4e8c3120ab43e814eadabd 100644
--- a/src/nf_modules/samtools/index_bams.config
+++ b/src/nf_modules/samtools/index_bams.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: index_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/sort_bams.config b/src/nf_modules/samtools/sort_bams.config
index 8d1153d249c06519d267e4b6efd568f3f26c7866..fd8a865574697b09986b82ed881a56e50f3f9cc8 100644
--- a/src/nf_modules/samtools/sort_bams.config
+++ b/src/nf_modules/samtools/sort_bams.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: sort_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/samtools/split_bams.config b/src/nf_modules/samtools/split_bams.config
index 7250173170413da238b64a89364d3548c12e9900..00a839483ad447a73bac23e7285de2b5b8b83ee5 100644
--- a/src/nf_modules/samtools/split_bams.config
+++ b/src/nf_modules/samtools/split_bams.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: split_bam {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/samtools_1.7"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/sratoolkit/fastqdump.config b/src/nf_modules/sratoolkit/fastqdump.config
index 664482e0908655bd77ecd76407d277d1a71b6235..a0347be814a451059a75462822b54c5cbe5c2a9b 100644
--- a/src/nf_modules/sratoolkit/fastqdump.config
+++ b/src/nf_modules/sratoolkit/fastqdump.config
@@ -35,7 +35,7 @@ profiles {
ccin2p3 {
process{
withName: fastq_dump {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/sratoolkit_2.8.2"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/urqt/trimming_paired.config b/src/nf_modules/urqt/trimming_paired.config
index 1b250b3967f4e1bd657a6880841691032a458a91..deedb874dc0a07c5a989b4293022670baa9f0ebd 100644
--- a/src/nf_modules/urqt/trimming_paired.config
+++ b/src/nf_modules/urqt/trimming_paired.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
scratch = true
stageInMode = "copy"
diff --git a/src/nf_modules/urqt/trimming_single.config b/src/nf_modules/urqt/trimming_single.config
index b107cf2271706a4e66c65b0ed5a8c53a8f74a650..7f7fdc56f06805c615a8a2117e5a20f96cf261ca 100644
--- a/src/nf_modules/urqt/trimming_single.config
+++ b/src/nf_modules/urqt/trimming_single.config
@@ -36,7 +36,7 @@ profiles {
ccin2p3 {
process{
withName: trimming {
- beforeScript = "sh /sps/lbmc/common/miniconda3/init.sh"
+ beforeScript = "source /sps/lbmc/common/miniconda3/init.sh"
conda = "/sps/lbmc/common/miniconda3/envs/urqt_d62c1f8"
scratch = true
stageInMode = "copy"