diff --git a/src/nf_modules/bedtools/fasta_from_bed.config b/src/nf_modules/bedtools/fasta_from_bed.config
index 574e6d730d097c14c6f690aca8d8bb83373373a7..d8dc120c93daae9550844ce32526a212006a5e3a 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 4b554a7bada09952e5b1c9bd26ebd5c09c09ea62..05d5c9412e598d26bbed994eb06caf50c81220d5 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 49eb9c53791cc79c0942f8979ca93a57348d20d4..99723a35422c8178bf768f627ef063450030154b 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 49eb9c53791cc79c0942f8979ca93a57348d20d4..99723a35422c8178bf768f627ef063450030154b 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 5ed9bcc390d5de7a367de78e285c537d76b5c7dc..6e9cef00c89357a072bfaf3e4e391b14e611c12a 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 bc1c8979a4b1bd7912be6310bcf79e7ea2c2be4e..48ba0b18e35f533be0843c7b37f93b0f7d570d18 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 bc1c8979a4b1bd7912be6310bcf79e7ea2c2be4e..48ba0b18e35f533be0843c7b37f93b0f7d570d18 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 4e89c3be04dd9e3ed81c685fce928bfcaac2a3f8..adee7793a98da076def5454b020a933204084d33 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 aebe28c5b07a34c6637e870761b8e28722f14fab..815292498a00be5f91cd62a8b430a29a3cca1f8e 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 8e62c1cc9cef35b46d88659056f2a033206f7c90..79818d9554cd58c09781d90345dc11e0cc7893b9 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 8e62c1cc9cef35b46d88659056f2a033206f7c90..79818d9554cd58c09781d90345dc11e0cc7893b9 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 f94b4e4822dc58128e8659a5ef3dd625ca2171fe..30faba103bd22a2a7682d476dd677f3e8caab5d0 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 f94b4e4822dc58128e8659a5ef3dd625ca2171fe..30faba103bd22a2a7682d476dd677f3e8caab5d0 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 13952d879c66d04353c679d1bd894b5f5130434c..ffb6271143ccbe15f04676f7cd487315e27cb469 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 ea4bab25f53e1fb14c55fd6e20803bd335547299..f6c49a3a7270d6790289c8841717f3b31af0faf6 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 184835474200415f46cc563a906c1bc89de23ce2..99ea5acb051a86a1913f0c885d45e6d2f4cf6f3b 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 6cece587f1332d33e95da86bb2772cfc2a1ef61f..b7e89b3463a900812c1b316f6c1069ebb03f5cac 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 6cece587f1332d33e95da86bb2772cfc2a1ef61f..b7e89b3463a900812c1b316f6c1069ebb03f5cac 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 6731be65d1cda3525b93163fa4084914c8cf8f0d..c0db2aa86a709df9e252680dfd82cc2b8ca71653 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 6731be65d1cda3525b93163fa4084914c8cf8f0d..c0db2aa86a709df9e252680dfd82cc2b8ca71653 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 01646ee1a4a38a6a80171e0fc97527162f89919d..443c33aff182cc21dbdb70e39b36f39aaf177217 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 8d1d44724f1d5b8edef967afa63c3222327f4a22..4840d58a87d93bf80149aa699276040a44f5d36f 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 8a038dd9bb069866ff152f05950ff45f889be6a7..fefa4c335fb4a9d3463b425a982a2b8cb886aef5 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 8ac5af00c53b74646bf0d320b50e3f2a9b72f0e7..dc990d3a929ccc3f6c538f5380efdeb59305e25e 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 8ac5af00c53b74646bf0d320b50e3f2a9b72f0e7..dc990d3a929ccc3f6c538f5380efdeb59305e25e 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 d9a72019ae48fe8c16bb4a41d6ec1715d27c4199..5122f5f65aecef415fb032e18a423554c0128d43 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 40754658a5d749d4d88aee2d286b0672809b3dde..e5329fc8435955b634573effa930e861f9b51301 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 f440d1463b8d6a5c04523f6a78fb31cc1b6ae291..d7239b9e4f0825163246cee3746a276fd608424a 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 d0841719696253cc65bd4ee614e144e7642674b3..e14192e5d95f56061551e558e2dc8e3361fa4519 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 d49f444a40326f18c6559e3de0a9a7364135cc03..851d0cfbf1a8a08bc5476fc74f6b608eb8d330c9 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 90eaae7075dc36b2a4a56371edf0968dda903044..a0589cb6578aab5b45588d73ed258bc5e1f1a73b 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 90eaae7075dc36b2a4a56371edf0968dda903044..a0589cb6578aab5b45588d73ed258bc5e1f1a73b 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 d1dd2c3ad3b93d85ebf87ce9cd18f581c41c3eda..d144dcb3a265718e75f9283eb253b7f5ede7b636 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 145fa48d189c0087aceb8d98bfe332f29a6d7ff5..896fb342542613f41bfd87628ed193dc3117606b 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 afd305f9b4d7ed52d2ad5d3e459da0a3793bd3d3..967a79a30a784fdcd4099c676d285f3dff776c36 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 0b4f093b1404216f0c6112684860f47d7c3bc14b..6dab50bcdf7e2b27371df68103761dff07d3b98c 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 69f9664feb4634b3a1a8d229fb194d5f5212e5d2..9d7dbe0f8c978cdf1a280c6be6e726d210123fb9 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 49bc53f8909f871beb3db423eca8854daaee4c5a..765e75e84d6fc26319c8a38ac41dba07dfb76263 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 8436342a6055c5a1490898971a5f6886afa550ec..f2b401c10a9e0884c58f7e53ce98d07d1c912c86 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 eb4468d9f018e356b79a420fd2c2127ce09908e5..0462310f9fc9816ca4ee4b8195dfe4d172418f70 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 ad33eec91395933e1fc94591957bd8ed8f60e4a8..924aa0d285d4d954cb3129a30e23ff422fb36364 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 4e8e0340007d862dfb34c64da5db853bd8364bf1..31675091b31d8f1cb047d92e79e38481b294f3a2 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 ccc103111df879be9112a2068f2bb86a3b38ccc9..e5e61dbdd59060daaac86032cbd8b106dfa9c905 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 a9806cebc95c8701ebb4d137178e12384b2a4e44..f70917233c63134405d52c0a10a796b3b8dc9ca9 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 deb62fecf60782206980557c3de7359db8b5a618..453e7b7e8b3e6632436943c5f8a3cfc8e315455d 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"