Changed Picard memory config and fix tmpdir path in BuildBamIndex (#24)

* Changed Picard memory config and fix tmpdir path in BuildBamIndex

* Put 'g' in params

Co-authored-by: bugh1 <>

Author: bugh1

pipeline/align-DNA.nf

@@ -23,6 +23,10 @@ if (amount_of_memory < 1) {
 }
 amount_of_memory = amount_of_memory.toString() + " GB"
 
+// Default memory configuration for Picard's Java commands
+params.mem_command_sort_sam = "4g"
+params.mem_command_mark_duplicates = "4g"
+params.mem_command_build_bam_index = "4g"
 
 // output details of the pipeline run to stdout
 log.info """\
@@ -217,7 +221,7 @@ process PicardTools_SortSam  {
    """
    set -euo pipefail
 
-   java -Xmx100g -Djava.io.tmpdir=/temp_dir \
+   java -Xmx${params.mem_command_sort_sam} -Djava.io.tmpdir=/temp_dir \
       -jar /picard-tools/picard.jar \
       SortSam \
       --VALIDATION_STRINGENCY LENIENT \
@@ -252,7 +256,7 @@ process PicardTools_MarkDuplicates  {
    # add picard option prefix, '--INPUT' to each input bam
    declare -r INPUT=$(echo '!{input_bams}' | sed -e 's/ / --INPUT /g' | sed '1s/^/--INPUT /')
 
-   java -Xmx100g -Djava.io.tmpdir=/temp_dir/ \
+   java -Xmx!{params.mem_command_mark_duplicates} -Djava.io.tmpdir=/temp_dir \
       -jar /picard-tools/picard.jar \
       MarkDuplicates \
       --VALIDATION_STRINGENCY LENIENT \
@@ -270,7 +274,7 @@ output_ch_PicardTools_MarkDuplicates
 // index bams with picard
 process PicardTools_BuildBamIndex  {
    container docker_image_PicardTools
-   containerOptions "--volume ${params.java_temp_dir}:/java_temp_dir"
+   containerOptions "--volume ${params.temp_dir}:/temp_dir"
 
    publishDir path: params.output_dir, mode: 'copy'
 
@@ -288,7 +292,7 @@ process PicardTools_BuildBamIndex  {
    """
    set -euo pipefail
 
-   java -Xmx100g -Djava.io.tmpdir=/java_temp_dir \
+   java -Xmx${params.mem_command_build_bam_index} -Djava.io.tmpdir=/temp_dir \
       -jar /picard-tools/picard.jar \
       BuildBamIndex \
       --VALIDATION_STRINGENCY LENIENT \