Fix Spark temp dir permissions (#145)

* Fix Spark temp dir permissions

* Bump version to 7.2.1

CHANGELOG.md

@@ -7,9 +7,13 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/).
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-
 ## [Unreleased]
 
+
+## [7.2.1] - 2021-10-28
+### Changed
+- Fix potential Spark temp directory permissions issue
+
 ## [7.2.0] - 2021-10-01
 ### Added
 - GPL2 License added

pipeline/config/methods.config

@@ -5,7 +5,7 @@ manifest {
     name = "align-DNA"
     author = "Benjamin Carlin; Chenghao Zhu; Aaron Holmes; Yash Patel"
     description = "alignment pipeline for paired fastqs DNA samples"
-    version = "7.2.0"
+    version = "7.2.1"
     }
 
 params {

pipeline/modules/mark_duplicates_spark.nf

@@ -38,7 +38,28 @@ process run_MarkDuplicatesSpark_GATK  {
       path "${params.sample_name}.mark_dup.metrics"
       path(".command.*")
 
-   beforeScript 'chmod 777 `pwd`'
+   //Update tempdir permissions for user 'nobody'
+   beforeScript "chmod 777 `pwd`; \
+      if [[ ! -d ${params.temp_dir} ]]; \
+      then \
+         mkdir -p ${params.temp_dir}; \
+         chmod 777 ${params.temp_dir}; \
+      else \
+         if [[ ! `stat -c %a ${params.temp_dir}` == 777 ]]; \
+         then \
+            chmod 777 ${params.temp_dir}; \
+         fi; \
+      fi; \
+      if [[ ! -d ${params.spark_temp_dir} ]]; \
+      then \
+         mkdir -p ${params.spark_temp_dir}; \
+         chmod 777 ${params.spark_temp_dir}; \
+      else \
+         if [[ ! `stat -c %a ${params.spark_temp_dir}` == 777 ]]; \
+         then \
+            chmod 777 ${params.spark_temp_dir}; \
+         fi; \
+      fi"
 
    shell:
    bam_output_filename = "${params.bam_output_filename}"