From 8ace68acf2c53e0d7065cb12259106d260a4fa6b Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Sun, 3 Nov 2024 09:06:59 -0800
Subject: [PATCH 01/15] emit gridss assembly

---
 module/gridss.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/module/gridss.nf b/module/gridss.nf
index a79b935..53933de 100644
--- a/module/gridss.nf
+++ b/module/gridss.nf
@@ -88,7 +88,7 @@ process run_assembly_GRIDSS {
 
     output:
         path "${tumor_id}.assembly.bam", emit: gridss_assembly_bam
-        path "${tumor_id}.assembly.bam.gridss.working/*"
+        path "${tumor_id}.assembly.bam.gridss.working/*", emit: gridss_assembly
         path ".command.*"
 
     script:

From b8f92eeecac0b644177303ece52d8e50fe9c16e2 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Sun, 3 Nov 2024 09:07:30 -0800
Subject: [PATCH 02/15] get parent dir for gridss assembly

---
 main.nf | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/main.nf b/main.nf
index b118c84..4f10284 100644
--- a/main.nf
+++ b/main.nf
@@ -217,6 +217,12 @@ workflow {
             gridss_reference_files,
             params.gridss_blacklist
             )
+
+        gridss_assembly_dir = preprocess_BAM_GRIDSS.out.gridss_assembly
+            .flatten()
+            .map { parentdir -> parentdir.getParent() }
+            .unique()
+            .collect()
         }
 
     }

From 49a03c35b9be4de9eba4a7b62bbf0b81a0fda789 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Sun, 3 Nov 2024 09:51:07 -0800
Subject: [PATCH 03/15] add GRIDSS SV calling

---
 module/gridss.nf | 66 ++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 66 insertions(+)

diff --git a/module/gridss.nf b/module/gridss.nf
index 53933de..0951c9c 100644
--- a/module/gridss.nf
+++ b/module/gridss.nf
@@ -118,3 +118,69 @@ process run_assembly_GRIDSS {
             ${tumor_bam}
         """
     }
+
+process call_sSV_GRIDSS {
+    container params.docker_image_gridss
+
+    publishDir "${params.workflow_output_dir}/output/",
+        pattern: "${tumor_id}.{vcf, vcf.idx}",
+        mode: "copy",
+        saveAs: {
+            "${output_filename}_${sanitize_string(file(it).getName().replace("${tumor_id}.", ""))}"
+            }
+
+    publishDir "${params.workflow_output_dir}/intermediate/${task.process.replace(':', '/')}",
+        pattern: "${tumor_id}.vcf.gridss.working/*",
+        mode: "copy",
+        saveAs: {
+            "${output_filename}.vcf.gridss.working/${output_filename}_${sanitize_string(file(it).getName().replace("${tumor_id}.", ""))}"
+            }
+
+    publishDir "${params.log_output_dir}/process-log",
+        pattern: ".command.*",
+        mode: "copy",
+        saveAs: { "${task.process.replace(':', '/')}/log${file(it).getName()}" }
+
+    input:
+        tuple(val(tumor_id), path(tumor_bam), path(tumor_bai), path(normal_bam), path(normal_bai))
+        path(gridss_preprocess_dir)
+        path(gridss_assembly_dir)
+        path(gridss_assembly_bam)
+        path(gridss_reference_fasta)
+        path(gridss_reference_files)
+        path(gridss_blacklist)
+
+    output:
+        path "${tumor_id}.vcf", emit: gridss_vcf
+        path "${tumor_id}.vcf.idx", emit: gridss_vcf_idx
+        path "${tumor_id}.vcf.gridss.working/*", emit: gridss_vcf_dir
+        path ".command.*"
+
+    script:
+        otherjvmheap = 4.GB
+        gridss_otherjvmheap = "${otherjvmheap.toGiga()}g"
+        gridss_jvmheap = "${(task.memory - otherjvmheap).toGiga()}g"
+        gridss_jar = "/usr/local/share/gridss-${params.gridss_version}-1/gridss.jar"
+        output_filename = generate_standard_filename(
+            "GRIDSS2-${params.gridss_version}",
+            params.dataset_id,
+            tumor_id,
+            [:]
+            )
+
+        """
+        set -euo pipefail
+        gridss \
+            -r ${gridss_reference_fasta} \
+            -j ${gridss_jar} \
+            -s call \
+            -t ${task.cpus} \
+            --jvmheap ${gridss_jvmheap} \
+            --otherjvmheap ${gridss_otherjvmheap} \
+            -b ${gridss_blacklist} \
+            -a ${gridss_assembly_bam} \
+            --output ${tumor_id}.vcf \
+            ${normal_bam} \
+            ${tumor_bam}
+        """
+    }

From 96557c497016b7a6e70451df426e4d987881880e Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Sun, 3 Nov 2024 09:52:36 -0800
Subject: [PATCH 04/15] add resource allocation for gridss sv calling in F16

---
 config/F16.config | 11 +++++++++++
 1 file changed, 11 insertions(+)

diff --git a/config/F16.config b/config/F16.config
index 7f5f57d..5d5b91d 100644
--- a/config/F16.config
+++ b/config/F16.config
@@ -26,6 +26,17 @@ process {
             }
         }
 
+    withName: call_sSV_GRIDSS {
+        cpus = 8
+        memory = 15.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 16.GB

From dec08ae811fe9ed192943203b9f210efd1169613 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Sun, 3 Nov 2024 09:56:39 -0800
Subject: [PATCH 05/15] add gridss SV calling to main

---
 main.nf | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/main.nf b/main.nf
index 4f10284..0269d57 100644
--- a/main.nf
+++ b/main.nf
@@ -225,4 +225,13 @@ workflow {
             .collect()
         }
 
+        call_sSV_GRIDSS(
+            input_paired_bams_ch,
+            gridss_assembly_dir,
+            run_assembly_GRIDSS.out.gridss_assembly_bam,
+            params.gridss_reference_fasta,
+            gridss_reference_files,
+            params.gridss_blacklist
+            )
+
     }

From a2423c28bc073aec55d18dd671ce60b384f56584 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Tue, 5 Nov 2024 10:36:12 -0800
Subject: [PATCH 06/15] fix naming format

---
 module/gridss.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/module/gridss.nf b/module/gridss.nf
index 0951c9c..19d9496 100644
--- a/module/gridss.nf
+++ b/module/gridss.nf
@@ -123,17 +123,17 @@ process call_sSV_GRIDSS {
     container params.docker_image_gridss
 
     publishDir "${params.workflow_output_dir}/output/",
-        pattern: "${tumor_id}.{vcf, vcf.idx}",
+        pattern: "${tumor_id}.{vcf,vcf.idx}",
         mode: "copy",
         saveAs: {
-            "${output_filename}_${sanitize_string(file(it).getName().replace("${tumor_id}.", ""))}"
+            "${output_filename}.${sanitize_string(file(it).getName().replace("${tumor_id}.", ""))}"
             }
 
     publishDir "${params.workflow_output_dir}/intermediate/${task.process.replace(':', '/')}",
         pattern: "${tumor_id}.vcf.gridss.working/*",
         mode: "copy",
         saveAs: {
-            "${output_filename}.vcf.gridss.working/${output_filename}_${sanitize_string(file(it).getName().replace("${tumor_id}.", ""))}"
+            "${output_filename}.vcf.gridss.working/${output_filename}.${sanitize_string(file(it).getName().replace("${tumor_id}.", ""))}"
             }
 
     publishDir "${params.log_output_dir}/process-log",

From 33ca0772571727b0b3954ecbab24456729ecdfc5 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Tue, 5 Nov 2024 10:40:04 -0800
Subject: [PATCH 07/15] fix call_sSV_GRIDSS function call

---
 main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/main.nf b/main.nf
index 0269d57..a47f59e 100644
--- a/main.nf
+++ b/main.nf
@@ -55,7 +55,7 @@ include { call_sSV_Delly; filter_sSV_Delly } from './module/delly' addParams(
 include { call_sSV_Manta } from './module/manta' addParams(
     workflow_output_dir: "${params.output_dir_base}/Manta-${params.manta_version}"
     )
-include { preprocess_BAM_GRIDSS; run_assembly_GRIDSS } from './module/gridss' addParams(
+include { preprocess_BAM_GRIDSS; run_assembly_GRIDSS; call_sSV_GRIDSS } from './module/gridss' addParams(
     workflow_output_dir: "${params.output_dir_base}/GRIDSS-${params.gridss_version}"
     )
 include { generate_sha512 as generate_sha512_BCFtools } from './module/sha512' addParams(
@@ -218,20 +218,20 @@ workflow {
             params.gridss_blacklist
             )
 
-        gridss_assembly_dir = preprocess_BAM_GRIDSS.out.gridss_assembly
+        gridss_assembly_dir = run_assembly_GRIDSS.out.gridss_assembly
             .flatten()
             .map { parentdir -> parentdir.getParent() }
             .unique()
             .collect()
-        }
 
         call_sSV_GRIDSS(
             input_paired_bams_ch,
+            gridss_preprocess_dir,
             gridss_assembly_dir,
             run_assembly_GRIDSS.out.gridss_assembly_bam,
             params.gridss_reference_fasta,
             gridss_reference_files,
             params.gridss_blacklist
             )
-
+        }
     }

From cb1a3131ccb1920dcd238061a1a13b6f2e3f6eee Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Tue, 5 Nov 2024 11:13:22 -0800
Subject: [PATCH 08/15] update CHANGELOG.md

---
 CHANGELOG.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index b6d1aee..6dc7a4a 100755
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -9,6 +9,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 ### Added
+- Add GRIDSS2 variant calling
 - Add GRIDSS2 assembly
 - Add GRIDSS2 preprocessing
 - Add supported Nextflow version to `README.md`

From 2d357d2e25305f95062722df4fb5447a4ea074c3 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Tue, 5 Nov 2024 11:14:05 -0800
Subject: [PATCH 09/15] fix spaces

---
 config/F2.config | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/config/F2.config b/config/F2.config
index 7727659..68120b8 100644
--- a/config/F2.config
+++ b/config/F2.config
@@ -36,7 +36,7 @@ process {
                 }
             }
         }
-    
+
     withName: call_sSV_Manta {
         cpus = 1
         memory = 3.GB
@@ -47,5 +47,4 @@ process {
                 }
             }
         }
-    } 
-
+    }

From dc7b3bc773cce03c58083688aaeec9e69ecbaba6 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Wed, 13 Nov 2024 15:17:22 -0800
Subject: [PATCH 10/15] parameterize other jvm heap

---
 config/template.config | 1 +
 module/gridss.nf       | 2 +-
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/config/template.config b/config/template.config
index 6971113..8b4c13c 100755
--- a/config/template.config
+++ b/config/template.config
@@ -16,6 +16,7 @@ params {
     // GRCh38 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed
     gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
     gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
+    other_jvm_heap = "4.GB"
 
     exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"
 
diff --git a/module/gridss.nf b/module/gridss.nf
index 19d9496..c34284f 100644
--- a/module/gridss.nf
+++ b/module/gridss.nf
@@ -157,7 +157,7 @@ process call_sSV_GRIDSS {
         path ".command.*"
 
     script:
-        otherjvmheap = 4.GB
+        otherjvmheap = params.other_jvm_heap
         gridss_otherjvmheap = "${otherjvmheap.toGiga()}g"
         gridss_jvmheap = "${(task.memory - otherjvmheap).toGiga()}g"
         gridss_jar = "/usr/local/share/gridss-${params.gridss_version}-1/gridss.jar"

From a13d8f9fb4ad917c11f1141f250b4a8a0dbc5890 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Wed, 13 Nov 2024 15:26:12 -0800
Subject: [PATCH 11/15] use other jvm heap parameter

---
 module/gridss.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/module/gridss.nf b/module/gridss.nf
index c34284f..6f0750e 100644
--- a/module/gridss.nf
+++ b/module/gridss.nf
@@ -92,7 +92,7 @@ process run_assembly_GRIDSS {
         path ".command.*"
 
     script:
-        otherjvmheap = 4.GB
+        otherjvmheap = params.other_jvm_heap
         gridss_otherjvmheap = "${otherjvmheap.toGiga()}g"
         gridss_jvmheap = "${(task.memory - otherjvmheap).toGiga()}g"
         gridss_jar = "/usr/local/share/gridss-${params.gridss_version}-1/gridss.jar"

From 9e3d7c3bba0cc78c6ecba1a4b17053808eef2b81 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Wed, 13 Nov 2024 15:35:17 -0800
Subject: [PATCH 12/15] add node configs

---
 config/F32.config | 11 +++++++++++
 config/F72.config | 11 +++++++++++
 config/M64.config | 11 +++++++++++
 3 files changed, 33 insertions(+)

diff --git a/config/F32.config b/config/F32.config
index 27604ab..e44941d 100644
--- a/config/F32.config
+++ b/config/F32.config
@@ -26,6 +26,17 @@ process {
             }
         }
 
+    withName: call_sSV_GRIDSS {
+        cpus = 8
+        memory = 30.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 30.GB
diff --git a/config/F72.config b/config/F72.config
index 6f7835c..0c01903 100644
--- a/config/F72.config
+++ b/config/F72.config
@@ -26,6 +26,17 @@ process {
             }
         }
 
+    withName: call_sSV_GRIDSS {
+        cpus = 8
+        memory = 30.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 30.GB
diff --git a/config/M64.config b/config/M64.config
index 29e2494..01c71d6 100644
--- a/config/M64.config
+++ b/config/M64.config
@@ -26,6 +26,17 @@ process {
             }
         }
 
+    withName: call_sSV_GRIDSS {
+        cpus = 8
+        memory = 120.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 120.GB

From acadc14bdadd03ab3c651ec60229061a244b1323 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Wed, 13 Nov 2024 15:52:44 -0800
Subject: [PATCH 13/15] enable save_intermediate_files option

---
 module/gridss.nf | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/module/gridss.nf b/module/gridss.nf
index 6f0750e..ea6a5d6 100644
--- a/module/gridss.nf
+++ b/module/gridss.nf
@@ -14,6 +14,7 @@ process preprocess_BAM_GRIDSS {
     container params.docker_image_gridss
 
     publishDir "${params.workflow_output_dir}/intermediate/${task.process.replace(':', '/')}",
+        enabled: params.save_intermediate_files,
         pattern: "${bam_name}.gridss.working/*",
         mode: "copy",
         saveAs: {
@@ -61,6 +62,7 @@ process run_assembly_GRIDSS {
     container params.docker_image_gridss
 
     publishDir "${params.workflow_output_dir}/intermediate/${task.process.replace(':', '/')}",
+        enabled: params.save_intermediate_files,
         pattern: "${tumor_id}.assembly.bam",
         mode: "copy",
         saveAs: {
@@ -68,6 +70,7 @@ process run_assembly_GRIDSS {
             }
 
     publishDir "${params.workflow_output_dir}/intermediate/${task.process.replace(':', '/')}",
+        enabled: params.save_intermediate_files,
         pattern: "${tumor_id}.assembly.bam.gridss.working/*",
         mode: "copy",
         saveAs: {
@@ -130,6 +133,7 @@ process call_sSV_GRIDSS {
             }
 
     publishDir "${params.workflow_output_dir}/intermediate/${task.process.replace(':', '/')}",
+        enabled: params.save_intermediate_files,
         pattern: "${tumor_id}.vcf.gridss.working/*",
         mode: "copy",
         saveAs: {

From f1e0a459ee0080221ff322eb6c85a6f63c9a729e Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Wed, 13 Nov 2024 17:24:05 -0800
Subject: [PATCH 14/15] remove double quotes for hother_jvm_heap

---
 config/template.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config/template.config b/config/template.config
index 8b4c13c..1174475 100755
--- a/config/template.config
+++ b/config/template.config
@@ -16,7 +16,7 @@ params {
     // GRCh38 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed
     gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
     gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
-    other_jvm_heap = "4.GB"
+    other_jvm_heap = 4.GB
 
     exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"
 

From c2ba27d2f26817678c0af026ef23b1dcdd1f2059 Mon Sep 17 00:00:00 2001
From: Faizal-Eeman <mmootor@mednet.ucla.edu>
Date: Wed, 20 Nov 2024 11:27:41 -0800
Subject: [PATCH 15/15] set other_jvm_heap in default config and document in
 template.config

---
 config/default.config  | 2 ++
 config/template.config | 3 ++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/config/default.config b/config/default.config
index c1496d9..14512e7 100644
--- a/config/default.config
+++ b/config/default.config
@@ -16,6 +16,8 @@ params {
     min_cpus = 1
     min_memory = 1.MB
 
+    other_jvm_heap = 4.GB
+
     cache_intermediate_pipeline_steps = false
 
     ucla_cds = true
diff --git a/config/template.config b/config/template.config
index 1174475..9bf6224 100755
--- a/config/template.config
+++ b/config/template.config
@@ -16,7 +16,8 @@ params {
     // GRCh38 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed
     gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
     gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
-    other_jvm_heap = 4.GB
+    // When GRIDSS errors OutOfMemory, update `other_jvm_heap`. Default is `4.GB`
+    //other_jvm_heap = 4.GB
 
     exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"