nf: change psmn config to use conda

src/conda_psmn.sh

+#!/bin/sh
+CONDA_PATH=/Xnfs/lbmcdb/common/conda/
+source ${CONDA_PATH}init.sh
+CONDA_ENVS=${CONDA_PATH}/envs/
+

src/nf_modules/bedtools/fasta_from_bed.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fasta_from_bed {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bedtools/2.25.0"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bedtools_2.25.0"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/bowtie/indexing.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bowtie_1.2.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         memory = "20GB"

src/nf_modules/bowtie/mapping_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2:samtools/1.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bowtie/1.2.2:samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/bowtie/mapping_single.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie/1.2.2:samtools/1.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bowtie/1.2.2:samtools_1.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/bowtie2/indexing.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/bowtie2/mapping_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/bowtie2/mapping_single.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bowtie2/2.3.4.1:samtools/1.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bowtie2_2.3.4.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/bwa/indexing.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: index_fasta {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bwa/0.7.17"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bwa_0.7.17"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/bwa/mapping_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: mapping_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "bwa/0.7.17"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "bwa_0.7.17"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/cutadapt/adaptor_removal_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: adaptor_removal {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/cutadapt/adaptor_removal_single.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: adaptor_removal {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/cutadapt/trimming_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/cutadapt/trimming_single.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: trimming {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "cutadapt/2.1"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "cutadapt_2.1"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/deeptools/bam_to_bigwig.config

@@ -30,8 +30,8 @@ profiles {
   psmn{
     process{
       withName: index_bam {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "sambamba/0.6.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "sambamba_0.6.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/deeptools/compute_matrix.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: compute_matrix {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deeptools/3.0.2"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "deeptools_3.0.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/deeptools/plot_profile.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: plot_profile {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "deeptools/3.0.2"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "deeptools_3.0.2"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 16

src/nf_modules/fastp/fastp_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fastp_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastp/0.19.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "fastp_0.19.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/fastp/fastp_single.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fastp_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastp/0.19.7"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "fastp_0.19.7"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1

src/nf_modules/fastqc/fastqc_paired.config

@@ -22,8 +22,8 @@ profiles {
   psmn{
     process{
       withName: fastqc_fastq {
-        beforeScript = "source /usr/share/lmod/lmod/init/bash; module use ~/privatemodules"
-        module = "fastqc/0.11.5"
+        beforeScript = "./src/conda_psmn.sh"
+        conda = "fastqc_0.11.5"
         executor = "sge"
         clusterOptions = "-cwd -V"
         cpus = 1