From 4800694d655a9457c70758ea38a426a3ab134e8e Mon Sep 17 00:00:00 2001
From: Mike Lloyd <mike.lloyd@jax.org>
Date: Tue, 8 Oct 2024 14:42:26 -0400
Subject: [PATCH] gridss-assembly-fix

---
 ReleaseNotes.md                   | 3 +++
 modules/gridss/gridss_assemble.nf | 7 ++++---
 nextflow.config                   | 2 +-
 3 files changed, 8 insertions(+), 4 deletions(-)

diff --git a/ReleaseNotes.md b/ReleaseNotes.md
index daad9dc..5055064 100644
--- a/ReleaseNotes.md
+++ b/ReleaseNotes.md
@@ -1,5 +1,8 @@
 # RELEASE NOTES
 
+## Release 0.7.4
+
+In this release we correct a nextflow issue in the GRIDSS_ASSEMBLY step used in the human PTA workflow.    
 
 ## Release 0.7.3
 
diff --git a/modules/gridss/gridss_assemble.nf b/modules/gridss/gridss_assemble.nf
index 465579d..c3d1d2d 100644
--- a/modules/gridss/gridss_assemble.nf
+++ b/modules/gridss/gridss_assemble.nf
@@ -15,9 +15,10 @@ process GRIDSS_ASSEMBLE {
     tuple val(sampleID), path('gridss_assemble/'), emit: gridss_assembly
 
     script:
-    String my_mem = (task.memory-1.GB).toString()
+    String my_mem = (task.memory-5.GB).toString()
+    String my_other_mem = (task.memory-30.GB).toString()
     heap_mem =  my_mem[0..-4]+'g'
-    other_mem = my_mem[0..-30]+'g'
+    other_mem = my_other_mem[0..-4]+'g'
 
     output_dir = 'gridss_assemble/'
 
@@ -43,4 +44,4 @@ process GRIDSS_ASSEMBLE {
     --picardoptions VALIDATION_STRINGENCY=LENIENT \
     ${normal_bam} ${tumor_bam}
     """
-}
\ No newline at end of file
+}
diff --git a/nextflow.config b/nextflow.config
index 1a6716d..d17efd9 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -45,7 +45,7 @@ manifest {
     homePage = "https://github.com/TheJacksonLaboratory/cs-nf-pipelines"
     mainScript = "main.nf"
     nextflowVersion = "!>=22.04.3"
-    version = "0.7.3"
+    version = "0.7.4"
     author = 'Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Tejas Temker, Anuj Srivastava. Copyright Jackson Laboratory 2024'
 }