Merge pull request #160 from uclahs-cds/jieunoh-update-picard-to-2.26.10

Jieunoh update picard to 2.26.10

Author: graceooh

CHANGELOG.md

@@ -10,6 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [Unreleased]
 ### Changed
 - Update GATK to 4.2.4.1 to address Log4j vulnerabilities (https://github.com/advisories/GHSA-8489-44mv-ggj8, https://github.com/advisories/GHSA-p6xc-xr62-6r2g)
+- Update Picard version to 2.26.10 to address Log4j moderate vulnerability (https://github.com/advisories/GHSA-8489-44mv-ggj8)
 
 ### Added
 - Add F32 config file

pipeline/config/F32.config

@@ -14,7 +14,7 @@ process {
         cpus = 32
         }
     withName: run_SortSam_Picard {
-        cpus = 1
+        cpus = 2
         memory = 10.GB
         }
     withName: run_MarkDuplicate_Picard {

pipeline/config/F72.config

@@ -14,7 +14,7 @@ process {
         cpus = 56
         }
     withName: run_SortSam_Picard {
-        cpus = 1
+        cpus = 2
         memory = 10.GB
         }
     withName: run_MarkDuplicate_Picard {

pipeline/config/M64.config

@@ -14,7 +14,7 @@ process {
         cpus = 56
         }
     withName: run_SortSam_Picard {
-        cpus = 1
+        cpus = 2
         memory = 10.GB
         }
     withName: run_MarkDuplicate_Picard {

pipeline/config/methods.config

@@ -15,7 +15,7 @@ params {
 
     docker_image_bwa_and_samtools = "blcdsdockerregistry/bwa-mem2_samtools-1.12:2.2.1"
     docker_image_hisat2_and_samtools = "blcdsdockerregistry/hisat2_samtools-1.12:2.2.1"
-    docker_image_picardtools = "blcdsdockerregistry/align-dna:picardtools-2.23.3"
+    docker_image_picardtools = "blcdsdockerregistry/picard:2.26.10"
     docker_image_sha512sum = "blcdsdockerregistry/align-dna:sha512sum-1.0"
     docker_image_validate_params = "blcdsdockerregistry/validate:2.1.5"    
     docker_image_gatk = "broadinstitute/gatk:4.2.4.1"
@@ -54,10 +54,6 @@ else {
 if (!params.containsKey('mark_duplicates')) {
     params.mark_duplicates = true
     }
-    
-params.mem_command_sort_sam = "4g"
-params.mem_command_mark_duplicates = "4g"
-params.mem_command_build_bam_index = "4g"
 
 docker {
     _uid_and_gid = "-u \$(id -u):\$(id -g)"

pipeline/modules/mark_duplicate_picardtools.nf

@@ -38,8 +38,8 @@ process run_MarkDuplicate_Picard {
    # add picard option prefix, '--INPUT' to each input bam
    declare -r INPUT=$(echo '!{input_bams}' | sed -e 's/ / --INPUT /g' | sed '1s/^/--INPUT /')
 
-   java -Xmx!{params.mem_command_mark_duplicates} -Djava.io.tmpdir=/temp_dir \
-      -jar /picard-tools/picard.jar \
+   java -Xmx${task.memory.getMega()}m -Djava.io.tmpdir=/temp_dir \
+      -jar /usr/local/share/picard-slim-2.26.10-0/picard.jar \
       MarkDuplicates \
       --VALIDATION_STRINGENCY LENIENT \
       $INPUT \

pipeline/modules/sort_bam_picardtools.nf

@@ -59,8 +59,8 @@ process run_SortSam_Picard  {
    """
    set -euo pipefail
 
-   java -Xmx${params.mem_command_sort_sam} -Djava.io.tmpdir=/temp_dir \
-      -jar /picard-tools/picard.jar \
+   java -Xmx${task.memory.getMega()}m -Djava.io.tmpdir=/temp_dir \
+      -jar /usr/local/share/picard-slim-2.26.10-0/picard.jar \
       SortSam \
       --VALIDATION_STRINGENCY LENIENT \
       --INPUT ${input_bam} \