Merge branch 'main' of github.com:uclahs-cds/pipeline-call-sSNV into …

…sfitz-nftest-assertions

CHANGELOG.md

@@ -6,7 +6,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+### Added
+- Add check for MuSE or Mutect2 on F2 node
+
 ### Changed
+- Fix blarchive compression log output directory
 - Delay readcount compression until original file is no longer needed
 
 ## [7.0.0-rc.1] - 2023-08-28

main.nf

@@ -47,6 +47,17 @@ log.info """\
         tumor_only_mode: ${params.tumor_only_mode}
 """
 
+if (params.max_cpus < 16 || params.max_memory < 30) {
+    if (params.algorithm.contains('muse') || params.algorithm.contains('mutect2')) {
+        error """\
+        ------------------------------------
+        ERROR: Insufficient resources: ${params.max_cpus} CPUs and ${params.max_memory} of memory.
+        ------------------------------------
+        To run Mutect2 or MuSE. this pipeline requires at least 16 CPUs and 32 GB of memory.
+        """
+        }
+    }
+
 include { 
     run_GetSampleName_Mutect2 as run_GetSampleName_Mutect2_normal
     run_GetSampleName_Mutect2 as run_GetSampleName_Mutect2_tumor 

module/common.nf

@@ -88,7 +88,7 @@ process compress_file_blarchive {
     set -euo pipefail
     dereferenced_file=\$(readlink -f ${file_to_compress})
     blarchive compress_files --input \$dereferenced_file \
-        --log ${params.work_dir}
+        --log ./
     ln -s \${dereferenced_file}.bz2 ${file_to_compress}.bz2
     """
     }