define conda dependencies at process level

TRON-Bioinformatics · Nov 8, 2021 · c3f5308 · c3f5308
1 parent ff0cf30
commit c3f5308
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Showing 6 changed files with 23 additions and 26 deletions.
diff --git a/Dockerfile b/Dockerfile
diff --git a/environment.yml b/environment.yml
diff --git a/modules/bwa_aln.nf b/modules/bwa_aln.nf
@@ -1,13 +1,16 @@
 params.cpus = 8
 params.memory = "8g"
 params.reference = false
+params.enable_conda = false
 
 
 process BWA_ALN {
     cpus "${params.cpus}"
     memory "${params.memory}"
     tag "${name}"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
         tuple val(name), file(fastq)
 
@@ -25,6 +28,8 @@ process BWA_SAMPE {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(sai1), file(fastq2), file(sai2)
@@ -43,6 +48,8 @@ process BWA_SAMSE {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq), file(sai)
@@ -61,6 +68,8 @@ process BWA_ALN_INCEPTION {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(fastq2)

diff --git a/modules/bwa_mem.nf b/modules/bwa_mem.nf
@@ -1,6 +1,7 @@
 params.cpus = 8
 params.memory = "8g"
 params.reference = false
+params.enable_conda = false
 
 
 process BWA_MEM {
@@ -9,6 +10,8 @@ process BWA_MEM {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq1), file(fastq2)
@@ -27,6 +30,8 @@ process BWA_MEM_SE {
     tag "${name}"
     publishDir params.output, mode: "move"
 
+    conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.12" : null)
+
     input:
       // joins both channels by key using the first element in the tuple, the name
       tuple val(name), file(fastq)

diff --git a/modules/fastp.nf b/modules/fastp.nf
@@ -1,13 +1,17 @@
 params.memory = "3g"
 params.cpus = 1
 params.output = "."
+params.enable_conda = false
+params.enable_docker = true
 
 
 process FASTP_PAIRED {
     cpus params.cpus
     memory params.memory
     publishDir "${params.output}", mode: "copy", pattern: "*fastp_stats*"
 
+    conda (params.enable_conda ? "bioconda::fastp=0.20.1" : null)
+
     input:
         tuple val(name), file(fastq1), file(fastq2)
 
@@ -34,6 +38,8 @@ process FASTP_SINGLE {
     memory params.memory
     publishDir "${params.output}", mode: "copy", pattern: "*fastp_stats*"
 
+    conda (params.enable_conda ? "bioconda::fastp=0.20.1" : null)
+
     input:
         tuple val(name), file(fastq1)
 

diff --git a/nextflow.config b/nextflow.config
@@ -4,9 +4,10 @@
  * -------------------------------------------------
  */
 
-
 profiles {
-  conda { process.conda = "$baseDir/environment.yml" }
+  conda {
+    params.enable_conda = true
+  }
   debug { process.beforeScript = 'echo $HOSTNAME' }
   test {
     params.input_files = "test_data/test_input_paired.txt"