From f63cae028ce4421e4a491e52e193152e8af45b05 Mon Sep 17 00:00:00 2001
From: Mike Lloyd <mike.lloyd@jax.org>
Date: Thu, 2 May 2024 12:00:30 -0400
Subject: [PATCH] pta script fix. oom fixes

---
 ReleaseNotes.md                     | 4 ++++
 bin/pta/merge-caller-vcfs.r         | 5 +++--
 modules/picard/picard_reordersam.nf | 2 +-
 modules/r/annotate_sv.nf            | 4 ++--
 modules/r/annotate_sv_mouse.nf      | 4 ++--
 nextflow.config                     | 2 +-
 6 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/ReleaseNotes.md b/ReleaseNotes.md
index e3af53c..5484b84 100644
--- a/ReleaseNotes.md
+++ b/ReleaseNotes.md
@@ -1,5 +1,9 @@
 # RELEASE NOTES
 
+## Release 0.6.2
+
+In this minor release we adjust memory and wall clock statements, and modified `bin/pta/merge-caller-vcfs.r` to correct for an edge case related bug.
+
 ## Release 0.6.1
 
 In this minor release we added support for automatic Zenodo releases via github actions. There are no changes or additions to workflows.
diff --git a/bin/pta/merge-caller-vcfs.r b/bin/pta/merge-caller-vcfs.r
index fbefde4..9d9053a 100644
--- a/bin/pta/merge-caller-vcfs.r
+++ b/bin/pta/merge-caller-vcfs.r
@@ -1,6 +1,6 @@
 ## BJS Note: this script was located in the root path of the Docker container
 ## gcr.io/nygc-public/sv_cnv@sha256:1c14a50d131323a2a4bab323cf224879776af8de37f93df79292fd2e63269274
-## It is reproduced below as it exists there without modification
+## It is reproduced below with modification
 
 ## Merge arbitrary number of VCFs, annotate with simple event type 
 libs = c('optparse', 'StructuralVariantAnnotation', 'VariantAnnotation', 'rtracklayer', 'stringr')
@@ -264,7 +264,8 @@ mergeCallsets = function(a, b, slop) {
   
   ## Pull in non-matching SVs from b
   res = c(a, b[-subjectHits(overlaps)])
-
+  res = subset(res, (names(res) %in% res$partner) & (res$partner %in% names(res)))
+  
   return(res)
   
 }
diff --git a/modules/picard/picard_reordersam.nf b/modules/picard/picard_reordersam.nf
index 6b28d9a..9c4f62b 100644
--- a/modules/picard/picard_reordersam.nf
+++ b/modules/picard/picard_reordersam.nf
@@ -2,7 +2,7 @@ process PICARD_REORDERSAM {
     tag "$sampleID"
 
     cpus 1
-    memory 35.GB
+    memory 50.GB
     time '06:00:00'
     errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'}
 
diff --git a/modules/r/annotate_sv.nf b/modules/r/annotate_sv.nf
index 71a12ae..b84cf25 100644
--- a/modules/r/annotate_sv.nf
+++ b/modules/r/annotate_sv.nf
@@ -2,8 +2,8 @@ process ANNOTATE_SV {
   tag "$sampleID"
 
   cpus 1
-  memory 8.GB
-  time '04:00:00'
+  memory 10.GB
+  time '08:00:00'
   errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'}
 
   container 'quay.io/jaxcompsci/r-sv_cnv_annotate:4.1.1'
diff --git a/modules/r/annotate_sv_mouse.nf b/modules/r/annotate_sv_mouse.nf
index c2c02a5..cc82350 100644
--- a/modules/r/annotate_sv_mouse.nf
+++ b/modules/r/annotate_sv_mouse.nf
@@ -2,8 +2,8 @@ process ANNOTATE_SV {
   tag "$sampleID"
 
   cpus 1
-  memory 8.GB
-  time '04:00:00'
+  memory 10.GB
+  time '08:00:00'
   errorStrategy {(task.exitStatus == 140) ? {log.info "\n\nError code: ${task.exitStatus} for task: ${task.name}. Likely caused by the task wall clock: ${task.time} or memory: ${task.memory} being exceeded.\nAttempting orderly shutdown.\nSee .command.log in: ${task.workDir} for more info.\n\n"; return 'finish'}.call() : 'finish'}
 
   container 'quay.io/jaxcompsci/r-sv_cnv_annotate:4.1.1'
diff --git a/nextflow.config b/nextflow.config
index 8fd3687..c479adc 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 = "0.6.1"
+    version = "0.6.2"
     author = 'Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Anuj Srivastava. Copyright Jackson Laboratory 2024'
 }