Merge branch 'develop' into 'master'

Release v1.3.1 See merge request tron/tron-bam-preprocessing!14
TRON-Bioinformatics · May 16, 2021 · 6c2b617 · 6c2b617
2 parents fc59781 + 1fa0e4f
commit 6c2b617
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Showing 4 changed files with 18 additions and 10 deletions.
diff --git a/README.md b/README.md
@@ -45,7 +45,7 @@ This can be built from a BED file using Picard's BedToIntervalList (https://gatk
 ## How to run it
 
 ```
-$ nextflow run tron-bioinformatics/tronflow-bam-preprocessing -r v1.2.1 --help
+$ nextflow run tron-bioinformatics/tronflow-bam-preprocessing -r v1.3.1 --help
 N E X T F L O W  ~  version 19.07.0
 Launching `main.nf` [intergalactic_shannon] - revision: e707c77d7b
 
@@ -87,6 +87,8 @@ Computational resources:
     * --realignment_around_indels_memory: (default: 32g)
     * --bqsr_cpus: (default: 3)
     * --bqsr_memory: (default: 4g)
+    * --metrics_cpus: (default: 1)
+    * --metrics_memory: (default: 8g)
 
  Output:
     * Preprocessed and indexed BAMs

diff --git a/environment.yml b/environment.yml
@@ -1,6 +1,6 @@
 # You can use this file to create a conda environment for this pipeline:
 #   conda env create -f environment.yml
-name: tronflow-bam-preprocessing-1.3.0
+name: tronflow-bam-preprocessing-1.3.1
 channels:
   - conda-forge
   - bioconda

diff --git a/main.nf b/main.nf
@@ -28,6 +28,8 @@ params.realignment_around_indels_cpus = 2
 params.realignment_around_indels_memory = "32g"
 params.bqsr_cpus = 3
 params.bqsr_memory = "4g"
+params.metrics_cpus = 1
+params.metrics_memory = "8g"
 
 
 
@@ -155,8 +157,8 @@ if (! params.skip_metrics) {
     if (params.intervals) {
 
         process hsMetrics {
-            cpus 1
-            memory "2g"
+            cpus "${params.metrics_cpus}"
+            memory "${params.metrics_memory}"
             tag "${name}"
             publishDir "${publish_dir}/${name}/metrics", mode: "copy"
 
@@ -184,7 +186,7 @@ if (! params.skip_metrics) {
             mkdir tmp
 
             gatk CollectHsMetrics \
-            --java-options '-Xmx2g  -Djava.io.tmpdir=tmp' \
+            --java-options '-Xmx${params.metrics_memory}  -Djava.io.tmpdir=tmp' \
             --INPUT  ${bam} \
             --OUTPUT ${bam.baseName} \
             --TARGET_INTERVALS ${params.intervals} \
@@ -195,8 +197,8 @@ if (! params.skip_metrics) {
     }
 
     process metrics {
-	    cpus 1
-        memory "2g"
+	    cpus "${params.metrics_cpus}"
+        memory "${params.metrics_memory}"
 	    tag "${name}"
 	    publishDir "${publish_dir}/${name}/metrics", mode: "copy"
 
@@ -211,7 +213,7 @@ if (! params.skip_metrics) {
 	    mkdir tmp
 
 	    gatk CollectMultipleMetrics \
-        --java-options '-Xmx2g  -Djava.io.tmpdir=tmp' \
+        --java-options '-Xmx${params.metrics_memory}  -Djava.io.tmpdir=tmp' \
         --INPUT  ${bam} \
         --OUTPUT ${bam.baseName} \
         --REFERENCE_SEQUENCE ${params.reference} \

diff --git a/nextflow.config b/nextflow.config
@@ -21,6 +21,8 @@ profiles {
     params.realignment_around_indels_memory = "3g"
     params.bqsr_cpus = 1
     params.bqsr_memory = "3g"
+    params.metrics_cpus = 1
+    params.metrics_memory = "3g"
     params.known_indels1 = "$baseDir/test_data/1000G_phase1.indels.hg19.sites.minimal.vcf"
     params.known_indels2 = "$baseDir/test_data/Mills_and_1000G_gold_standard.indels.hg19.sites.sorted.minimal.vcf"
     params.intervals = "$baseDir/test_data/minimal_intervals.intervals"
@@ -55,12 +57,12 @@ dag {
   //file = "${params.output}/pipeline_dag.svg"
 }
 
-VERSION = '1.3.0'
+VERSION = '1.3.1'
 DOI = 'https://zenodo.org/badge/latestdoi/358400957'
 
 manifest {
   name = 'TRON-Bioinformatics/tronflow-bam-preprocessing'
-  author = 'Pablo Riesgo Ferreiro, Özlem Muslu'
+  author = 'Pablo Riesgo-Ferreiro, Özlem Muslu'
   homePage = 'https://github.com/TRON-Bioinformatics/tronflow-bam-preprocessing'
   description = 'Picard and GATK BAM preprocessing pipeline'
   mainScript = 'main.nf'
@@ -110,6 +112,8 @@ Computational resources:
     * --realignment_around_indels_memory: (default: 32g)
     * --bqsr_cpus: (default: 3)
     * --bqsr_memory: (default: 4g)
+    * --metrics_cpus: (default: 1)
+    * --metrics_memory: (default: 8g)
 
  Output:
     * Preprocessed and indexed BAMs