Add GRIDSS preprocessing (#175)

* add gridss nf module * add preprocess gridss BAM process and update I/O/Script section * add gridss version and docker * add preprocess_BAM_GRIDSS * add gridss_reference_diir param to template.config * input preprocess channels; set variables; publish formatted filenames * add gridss2 channels, ref and process call * add gridss2 to algorithhms in template * update schema YAML * add gridss ref dir to schema * Update CHANGELOG.md * update metadata.yaml * add jvmheap memory arg to gridss * 4 CPUs and 10GB memory for gridss preprocessing * change gridss ref dir to ref FASTA * change gridss ref dir to ref FASTA * reconfigure gridss ref files variable * fix gridss ref file path * store intermediate file files in their process and store sample files in sample dirs * save logs tintask index dir * add F32, F72 and M64 configs * update memory in F32, F72 and M64 --------- Co-authored-by: Mootor <mmootor@ip-0A125937.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
uclahs-cds · Oct 1, 2024 · 253dd16 · 253dd16
1 parent 94daa7c
commit 253dd16
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,15 +9,14 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ## [Unreleased]
 ### Added
+- Add GRIDSS2 preprocessing
 - Add supported Nextflow version to `README.md`
+- Add PlantUML diagram
 
 ### Changed
 - Update PlantUML action to `v1.0.1`
 - Update memory allocations in `M64.config`
 
-### Added
-- Add PlantUML diagram
-
 ---
 
 ## [6.1.0] - 2024-03-12

diff --git a/config/F16.config b/config/F16.config
@@ -4,6 +4,17 @@ process {
         memory = 1.GB
         }
 
+    withName: preprocess_BAM_GRIDSS {
+        cpus = 4
+        memory = 10.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 16.GB
@@ -36,7 +47,7 @@ process {
                 }
             }
         }
-    
+
     withName: call_sSV_Manta {
         cpus = 1
         memory = 16.GB

diff --git a/config/F32.config b/config/F32.config
@@ -4,6 +4,17 @@ process {
         memory = 1.GB
         }
 
+    withName: preprocess_BAM_GRIDSS {
+        cpus = 4
+        memory = 10.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 30.GB
@@ -36,7 +47,7 @@ process {
                 }
             }
         }
-    
+
     withName: call_sSV_Manta {
         cpus = 1
         memory = 30.GB

diff --git a/config/F72.config b/config/F72.config
@@ -4,6 +4,17 @@ process {
         memory = 1.GB
         }
 
+    withName: preprocess_BAM_GRIDSS {
+        cpus = 4
+        memory = 15.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 30.GB
@@ -36,7 +47,7 @@ process {
                 }
             }
         }
-    
+
     withName: call_sSV_Manta {
         cpus = 1
         memory = 30.GB

diff --git a/config/M64.config b/config/M64.config
@@ -4,6 +4,17 @@ process {
         memory = 1.GB
         }
 
+    withName: preprocess_BAM_GRIDSS {
+        cpus = 4
+        memory = 100.GB
+        retry_strategy {
+            memory {
+                strategy = 'exponential'
+                operand = 2
+                }
+            }
+        }
+
     withName: call_sSV_Delly {
         cpus = 1
         memory = 120.GB
@@ -36,7 +47,7 @@ process {
                 }
             }
         }
-    
+
     withName: call_sSV_Manta {
         cpus = 1
         memory = 30.GB

diff --git a/config/default.config b/config/default.config
@@ -27,12 +27,14 @@ params {
     // Pipeline tool versions
     delly_version = '1.2.6'
     manta_version = '1.6.0'
+    gridss_version = '2.13.2'
     bcftools_version = '1.15.1'
     pipeval_version = '4.0.0-rc.2'
 
     // Docker tool versions
     docker_image_delly = "${-> params.docker_container_registry}/delly:${params.delly_version}"
     docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}"
+    docker_image_gridss = "${-> params.docker_container_registry}/gridss:${params.gridss_version}"
     docker_image_bcftools = "${-> params.docker_container_registry}/bcftools:${params.bcftools_version}"
     docker_image_validate = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
     }

diff --git a/config/schema.yaml b/config/schema.yaml
@@ -8,6 +8,11 @@ reference_fasta:
   mode: 'r'
   required: true
   help: 'Absolute path to a reference FASTA file'
+gridss_reference_fasta:
+  type: 'Path'
+  mode: 'r'
+  required: true
+  help: 'Absolute path to GRIDSS2 reference FASTA file'
 exclusion_file:
   type: 'Path'
   mode: 'r'
@@ -20,9 +25,11 @@ algorithm:
   default:
     - delly
     - manta
+    - gridss2
   choices:
     - delly
     - manta
+    - gridss2
 output_dir:
   type: 'Path'
   mode: 'w'

diff --git a/config/template.config b/config/template.config
@@ -12,13 +12,14 @@ params {
     blcds_registered_dataset = false
 
     reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
+    gridss_reference_fasta = "/hot/ref/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
 
     exclusion_file = "/hot/ref/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"
 
     output_dir = "where/to/save/outputs/"
 
     // select the tool(s) to run
-    algorithm = [] // algorithm = ['delly', 'manta']
+    algorithm = [] // algorithm = ['delly', 'manta', 'gridss2']
 
     save_intermediate_files = false
 

diff --git a/main.nf b/main.nf
@@ -34,6 +34,7 @@ Current Configuration:
     DELLY: ${params.delly_version}
     BCFtools: ${params.bcftools_version}
     Manta: ${params.manta_version}
+    GRIDSS2: ${params.gridss_version}
     PipeVal: ${params.pipeval_version}
 
 ------------------------------------
@@ -54,6 +55,9 @@ 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 } 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(
     workflow_output_dir: "${params.output_dir_base}/DELLY-${params.delly_version}"
     )
@@ -74,10 +78,15 @@ Channel.from(params.samples_to_process)
     .map{ sample -> ['index': indexFile(sample.path)] + sample }
     .set{ input_ch_samples_with_index }
 
+Channel.from(params.samples_to_process)
+    .map{ sample -> [sample.id, sample.path, indexFile(sample.path)] }
+    .set{ gridss_ch }
+
 input_ch_samples_with_index
     .map{ sample -> [sample.path, sample.index] }
     .flatten()
     .set{ input_validation }
+
 if (params.verbose){
     input_validation.view()
     }
@@ -96,6 +105,9 @@ if (params.verbose){
 
 reference_fasta_index = "${params.reference_fasta}.fai"
 
+// Collect GRIDSS reference files
+gridss_reference_files = Channel.fromPath( "${params.gridss_reference_fasta}.*", checkIfExists: true ).collect()
+
 workflow {
     /**
     * Validate the input bams
@@ -106,7 +118,6 @@ workflow {
         name: 'input_validation.txt',
         storeDir: "${params.output_dir_base}/validation/run_validate_PipeVal"
         )
-
     /**
     * Call "delly call -x hg19.excl -o t1.bcf -g hg19.fa tumor1.bam normal1.bam" per paired (tumor sample, normal sample)
     * The sv are stored in call_sSV_Delly.out.nt_call_bcf
@@ -158,7 +169,6 @@ workflow {
             call_sSV_Delly.out.nt_call_bcf_csi,
             call_sSV_Delly.out.tumor_id
             )
-
         /**
         * Filter the output bcf from filter_sSV_Delly.
         * The default filter_condition is "FILTER=='PASS'", which filters out NonPass calls.
@@ -168,7 +178,6 @@ workflow {
             params.filter_condition,
             call_sSV_Delly.out.tumor_id
             )
-
         /**
         * Generate one sha512 checksum for DELLY's output files.
         */
@@ -189,4 +198,12 @@ workflow {
             call_sSV_Manta.out.manta_vcfs.flatten()
             )
         }
+    if ('gridss2' in params.algorithm) {
+        preprocess_BAM_GRIDSS(
+            gridss_ch,
+            params.gridss_reference_fasta,
+            gridss_reference_files
+            )
+        }
+
     }
diff --git a/metadata.yaml b/metadata.yaml
@@ -1,8 +1,8 @@
 ---
 category: "pipeline"
-description: "Nextflow pipeline to call somatic structural variants using DELLY and Manta"
+description: "Nextflow pipeline to call somatic structural variants using DELLY, Manta and GRIDSS2"
 maintainers: "Boutros Lab Infrastructure <[email protected]>"
 languages: ["Nextflow", "Docker"]
 dependencies: ["Java", "Nextflow", "Docker"]
 references: "https://uclahs.box.com/s/qfzr99sc8ntmfddn30ii62wx4273utoz"
-tools: ["Delly:v1.2.6", "Manta:v1.6.0", "BCFtools:v1.15.1", "PipeVal:v4.0.0-rc.2"]
+tools: ["Delly:v1.2.6", "Manta:v1.6.0", "GRIDSS2:v2.13.2", "BCFtools:v1.15.1", "PipeVal:v4.0.0-rc.2"]
diff --git a/module/gridss.nf b/module/gridss.nf
@@ -0,0 +1,58 @@
+#!/usr/bin/env nextflow
+
+log.info """\
+------------------------------------
+             G R I D S S 2
+------------------------------------
+Docker Images:
+- docker_image_gridss: ${params.docker_image_gridss}
+"""
+
+include { generate_standard_filename; sanitize_string } from '../external/pipeline-Nextflow-module/modules/common/generate_standardized_filename/main.nf'
+
+process preprocess_BAM_GRIDSS {
+    container params.docker_image_gridss
+
+    publishDir "${params.workflow_output_dir}/intermediate/${task.process.replace(':', '/')}",
+        pattern: "${bam_name}.gridss.working/*",
+        mode: "copy",
+        saveAs: {
+            "${output_filename}.gridss.working/${output_filename}.${sanitize_string(file(it).getName().replace("${bam_name}.", ""))}"
+            }
+
+    publishDir "${params.log_output_dir}/process-log",
+        pattern: ".command.*",
+        mode: "copy",
+        saveAs: { "${task.process.replace(':', '/')}/${task.process}-${task.index}/log${file(it).getName()}" }
+
+    input:
+        tuple(val(sample_id), path(sample_bam), path(sample_index))
+        path(gridss_reference_fasta)
+        path(gridss_reference_files)
+
+    output:
+        path "${bam_name}.gridss.working/*", emit: gridss_preprocess
+        path ".command.*"
+
+    script:
+        gridss_mem = "${task.memory.toGiga()}g"
+        gridss_jar = "/usr/local/share/gridss-${params.gridss_version}-1/gridss.jar"
+        bam_name = file(sample_bam).getName()
+        output_filename = generate_standard_filename(
+            "GRIDSS2-${params.gridss_version}",
+            params.dataset_id,
+            sample_id,
+            [:]
+            )
+
+        """
+        set -euo pipefail
+        gridss \
+            -r ${gridss_reference_fasta} \
+            -j ${gridss_jar} \
+            -s preprocess \
+            -t ${task.cpus} \
+            --jvmheap ${gridss_mem} \
+            ${sample_bam}
+        """
+    }