make conda dependencies more granular

TRON-Bioinformatics · Nov 20, 2021 · a44185b · a44185b
1 parent 4532efa
commit a44185b
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Showing 7 changed files with 17 additions and 11 deletions.
diff --git a/environment.yml b/environment.yml
diff --git a/modules/01_prepare_bam.nf b/modules/01_prepare_bam.nf
@@ -17,6 +17,8 @@ process PREPARE_BAM {
     memory "${params.prepare_bam_memory}"
     tag "${name}"
 
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+
     input:
     tuple val(name), val(type), file(bam)
 
@@ -57,6 +59,8 @@ process INDEX_BAM {
     memory "${params.index_memory}"
     tag "${name}"
 
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+
     input:
     tuple val(name), val(bam_name), val(type), file(bam)
 

diff --git a/modules/02_mark_duplicates.nf b/modules/02_mark_duplicates.nf
@@ -11,6 +11,8 @@ process MARK_DUPLICATES {
     tag "${name}"
     publishDir "${params.output}/${name}/metrics", mode: "copy", pattern: "*.dedup_metrics.txt"
 
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+
     input:
     tuple val(name), val(bam_name), val(type), file(bam)
 

diff --git a/modules/03_metrics.nf b/modules/03_metrics.nf
@@ -12,6 +12,8 @@ process HS_METRICS {
     tag "${name}"
     publishDir "${params.output}/${name}/metrics", mode: "copy"
 
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+
     input:
     tuple val(name), val(bam_name), val(type), file(bam), file(bai)
 
@@ -44,6 +46,8 @@ process METRICS {
     tag "${name}"
     publishDir "${params.output}/${name}/metrics", mode: "copy"
 
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+
     input:
     tuple val(name), val(bam_name), val(type), file(bam), file(bai)
 

diff --git a/modules/04_realignment_around_indels.nf b/modules/04_realignment_around_indels.nf
@@ -12,6 +12,10 @@ process REALIGNMENT_AROUND_INDELS {
     tag "${name}"
     publishDir "${params.output}/${name}", mode: "copy", pattern: "*.RA.intervals"
 
+    // NOTE: this dependency is fixed to GATK 3 as the realignment around indels is not anymore maintained in GATK 4
+    // but still for some reason for GATK 3 to work the dependency to GATK 4 is needed
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0 bioconda::gatk=3.8" : null)
+
     input:
     tuple val(name), val(bam_name), val(type), file(bam), file(bai)
 

diff --git a/modules/05_bqsr.nf b/modules/05_bqsr.nf
@@ -11,6 +11,8 @@ process BQSR {
     publishDir "${params.output}/${name}", mode: "copy"
     tag "${name}"
 
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.0.0" : null)
+
     input:
     tuple val(name), val(bam_name), val(type), file(bam), file(bai)
 

diff --git a/nextflow.config b/nextflow.config
@@ -6,7 +6,7 @@
  */
 
 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.txt"