From 306ecfcc5cefd5bb8f2f7a2449b95246448b2e12 Mon Sep 17 00:00:00 2001
From: Tanubrata Dey <tdey@nygenome.org>
Date: Fri, 9 Feb 2024 12:21:39 -0500
Subject: [PATCH] BugFix: Addresses chr mismatch issue for ASCAT

---
 bigpurple.config            | 46 +++++++++++++++++++++++++++++++++++++
 bin/ascat_seg.R             |  1 +
 conf/base.config            |  4 ++--
 modules/local/jabba/main.nf |  4 ++--
 4 files changed, 51 insertions(+), 4 deletions(-)
 create mode 100644 bigpurple.config

diff --git a/bigpurple.config b/bigpurple.config
new file mode 100644
index 0000000..822cb90
--- /dev/null
+++ b/bigpurple.config
@@ -0,0 +1,46 @@
+
+params {
+    config_profile_name           = 'mskilab-org NYU BigPurple Cluster Profile'
+    config_profile_description    = """
+				    mskilab-org NYU School of Medicine BigPurple cluster profile to run nf-JaBbA.
+				    !!Make sure to load both singularity/3.1 and squashfs-tools/4.3 before running nf-JaBbA with this profile!!
+				    Ideal to make work folder on scratch as it generates whole lot of temporary files to run the pipeline
+				    Make sure to submit the run as an SBATCH job since we don't own our own node at NYU yet!!
+				    """.stripIndent()	
+    config_profile_contact        = "Tanubrata Dey (tanubrata.dey@nyulangone.org)"
+    config_profile_url            = "https://www.mskilab.org/"
+
+    // Resources
+    max_memory = 700.GB
+    max_cpus = 256
+    max_time = 10.d
+}
+process {
+
+    // default SLURM node config
+    beforeScript = """
+        module load singularity/3.9.8
+        module load squashfs-tools/4.3
+	
+    """
+    .stripIndent()
+
+    executor='slurm'
+
+    // memory errors which should be retried. otherwise error out
+    errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' }
+    maxRetries    = 3
+    maxErrors     = '-1'
+
+}
+executor {
+    name = 'slurm'
+    queueSize = 500
+    submitRateLimit = '10 sec'
+}
+singularity {
+    enabled = true
+    autoMounts = true
+    cacheDir = "/gpfs/data/imielinskilab/singularity_files/nextflow_singularity_cache"
+}
+
diff --git a/bin/ascat_seg.R b/bin/ascat_seg.R
index 835a6df..ae2bacd 100644
--- a/bin/ascat_seg.R
+++ b/bin/ascat_seg.R
@@ -625,6 +625,7 @@
 
     if (grepl(pattern = "txt$", x = opt$variants)) {
         variants.dt = fread(opt$variants)
+    	variants.dt[[1]] <- gsub("chr","",variants.dt[[1]])
         variants.dt[, ":="(alt.count.n = as.numeric(as.character(alt.count.n)),
                            ref.count.n = as.numeric(as.character(ref.count.n)),
                            alt.count.t = as.numeric(as.character(alt.count.t)),
diff --git a/conf/base.config b/conf/base.config
index 5a1d56b..3090ba6 100644
--- a/conf/base.config
+++ b/conf/base.config
@@ -103,11 +103,11 @@ process {
     }
     withName: 'SVABA' {
         cpus            = 4
-        memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
+        memory          = { check_max( 72.GB * task.attempt, 'memory' ) }
         time            = 84.h
     }
     withName: 'GRIDSS' {
-        cpus            = { check_max( 8 * task.attempt, 'cpus' ) }
+        cpus            = { check_max( 4 * task.attempt, 'cpus' ) }
         memory          = { check_max( 72.GB * task.attempt, 'memory' ) }
         time            = 84.h
     }
diff --git a/modules/local/jabba/main.nf b/modules/local/jabba/main.nf
index f97e527..23c0242 100644
--- a/modules/local/jabba/main.nf
+++ b/modules/local/jabba/main.nf
@@ -3,8 +3,8 @@ process JABBA {
     label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        '/gpfs/commons/home/tdey/lab/singularity_files/nextflow_singularity_cache/mskilab-jabba_cplex-latest.img':
-        'mskilab/jabba:latest' }"
+        'docker://mskilab/jabba_cplex:latest':
+        'mskilab/jabba_cplex:latest' }"
 
     input:
     tuple val(meta), path(cov_rds)