subworkflow: fingerprint_gbcms

.github/skip_nf_test.json

@@ -1,5 +1,9 @@
 {
     "conda": [
+        "modules/msk/custom/fingerprintvcfparser",
+        "modules/msk/custom/fingerprintcontamination",
+        "modules/msk/custom/fingerprintcombine",
+        "modules/msk/custom/fingerprintcorrelation",
         "modules/msk/calculatenoise",
         "modules/msk/ppflagfixer",
         "modules/msk/facets",
@@ -28,6 +32,7 @@
         "modules/msk/phylowgs/parsecnvs",
         "modules/msk/pvmaf/concat",
         "modules/msk/pvmaf/tagtraceback",
+        "subworkflows/msk/fingerprint_gbcms",
         "subworkflows/msk/genome_nexus",
         "modules/msk/oncokb/mafannotate"
     ],

modules/msk/custom/fingerprintcombine/environment.yml

@@ -0,0 +1,11 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+- conda-forge
+- bioconda
+dependencies:
+- conda-forge::r-argparse=2.2.5
+- conda-forge::r-data.table=1.17.8
+- conda-forge::r-dplyr=1.1.4
+- conda-forge::r-plyr=1.8.9
+- conda-forge::r-tidyverse=2.0.0

modules/msk/custom/fingerprintcombine/main.nf

@@ -0,0 +1,57 @@
+process CUSTOM_FINGERPRINTCOMBINE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'docker://community.wave.seqera.io/library/r-argparse_r-data.table_r-dplyr_r-plyr_r-tidyverse:8c0daffb3624cb66':
+        'community.wave.seqera.io/library/r-argparse_r-data.table_r-dplyr_r-plyr_r-tidyverse:8c0daffb3624cb66' }"
+        //'	oras://community.wave.seqera.io/library/r-argparse_r-data.table_r-dplyr_r-plyr_r-tidyverse:d96a65055f79744c':
+
+
+    input:
+    tuple val(meta), path(fp_tsv), val(sample), val(genome_build), val(patient)
+    path(liftover_loci_mapping)
+
+    output:
+    tuple val(meta), path("*DPfilter_ALL_FP.txt")                         , emit: combined_fp_tsv
+    tuple val("${task.process}"), val('complete_FP_table.R'), val('0.1.0'), emit: versions_fingerprintcombine, topic: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    declare -a fp_tsv_list
+    declare -a sample_list
+    declare -a genome_build_list
+    declare -a patient_list
+    fp_tsv_list=(${fp_tsv.join(' ')})
+    sample_list=(${sample.join(' ')})
+    genome_build_list=(${genome_build.join(' ')})
+    patient_list=(${patient.join(' ')})
+    echo -e "sample_id\tgenome_build\tfp_tsv\tpatient" > input.tsv
+    for i in \$(seq 0 1 \$((\${#fp_tsv_list[@]}-1)) ) ; do
+        fp_tsv=\${fp_tsv_list[i]}
+        sample=\${sample_list[i]}
+        genome=\${genome_build_list[i]}
+        patient=\${patient_list[i]}
+        echo -e "\$sample\t\$genome\t\$fp_tsv\t\$patient"
+    done >> input.tsv
+
+    complete_FP_table.R \\
+        -i input.tsv \\
+        -l $liftover_loci_mapping \\
+        $args
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+
+    """
+    echo $args
+
+    touch XDPfilter_ALL_FP.txt
+    """
+}

modules/msk/custom/fingerprintcombine/meta.yml

@@ -0,0 +1,82 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "custom_fingerprintcombine"
+description: |
+  A module to combine multiple fingerprint TSV files into a single comprehensive
+  table, with optional liftover of loci coordinates.
+keywords:
+  - fingerprint
+  - qc
+  - loci
+  - tsv
+  - correlation
+tools:
+  - "custom":
+      description: "A custom R script to combine fingerprint TSV files"
+      homepage: "https://github.com/mskcc-omics-workflows/modules/tree/main/modules/msk/custom/fingerprintcombine/meta.yml"
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - fp_tsv:
+        type: file
+        description: |
+          Fingerprint TSV files to be combined.
+          Structure: [ val(sample), val(genome_build), path(fp_tsv) ]
+        ontologies: []
+    - sample:
+        type: string
+        description: Sample identifier corresponding to each fingerprint TSV file.
+    - genome_build:
+        type: string
+        description:
+          Genome build (e.g., hg19, hg38) corresponding to each fingerprint
+          TSV file.
+  - - liftover_loci_mapping:
+        type: file
+        description: |
+          A TSV file mapping original loci to liftover loci.
+          Format: original_chr, original_pos, liftover_chr, liftover_pos
+        pattern: "*.tsv"
+        ontologies:
+          - edam: http://edamontology.org/format_3475 # TSV
+output:
+  combined_fp_tsv:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*DPfilter_ALL_FP.txt":
+          type: file
+          description: Wide table combining all input fingerprint TSV files.
+          pattern: "*DPfilter_ALL_FP.txt"
+          ontologies:
+            - edam: http://edamontology.org/format_3750 # TSV
+  versions_fingerprintcombine:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - complete_FP_table.R:
+          type: string
+          description: The name of the tool
+      - 0.1.0:
+          type: string
+          description: Version of the custom script
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - complete_FP_table.R:
+          type: string
+          description: The name of the tool
+      - 0.1.0:
+          type: string
+          description: Version of the custom script
+authors:
+  - "@anoronh4"
+maintainers:
+  - "@anoronh4"

modules/msk/custom/fingerprintcombine/resources/usr/bin/complete_FP_table.R

@@ -0,0 +1,110 @@
+#! /usr/bin/env Rscript
+
+#-------------------------------------------------------------------------------
+# Script: complete_FP_table.R
+# Author: Erika Gedvilaite
+# Date:   2025-09-23
+# Version: 0.1.0
+#
+# Description: This script takes in standard fingerprint tables and combines
+# them into a single, wide table for downstream plotting and analysis.
+#
+# Annotation:
+#   - Input table should have three columns: sample_id, genome_build, fp_tsv
+#   - Genome build should be either "hg19" or "hg38" or "GRCh37" or "GRCh38"
+#     (case insensitive)
+#
+#-------------------------------------------------------------------------------
+
+
+rm(list=ls())
+
+library(argparse, quietly = T)
+library(plyr, quietly = T)
+library(dplyr, quietly = T)
+library(data.table, quietly = T)
+library(tidyverse, quietly = T)
+
+`%notin%` <- Negate(`%in%`)
+`%notlike%` <- Negate(`%like%`)
+
+parser = ArgumentParser(description = 'Generate FP tables for plotting')
+parser$add_argument('-i', '--input_table', required = TRUE,
+                    help = 'Input table with paths to individual fingerprint TSV files, sample ids, and genome build')
+parser$add_argument('-o', '--analysis_folder', required = FALSE, default = ".",
+                    help = 'Output folder')
+parser$add_argument('-l', '--loci_mapper', required = TRUE,
+                    help = 'Loci mapper file')
+parser$add_argument('-d', '--depth_filter', required = FALSE, default = 20,
+                    help = 'Depth filter to apply to individual fingerprint TSV files (default: 20)')
+args = parser$parse_args()
+
+
+
+message("Reading in Liftover file")
+
+hg19_hg38_mapper = fread(args$loci_mapper,header = T)
+hg19_hg38_mapper$Loci_hg19 = paste(hg19_hg38_mapper$GRCH37_CHROM,hg19_hg38_mapper$GRCH37_POS,sep=":")
+hg19_hg38_mapper$Loci_hg38 = paste(hg19_hg38_mapper$GRCH38_CHROM,hg19_hg38_mapper$GRCH38_POS,sep=":")
+hg19_hg38_mapper = hg19_hg38_mapper %>% select(Loci_hg19, Loci_hg38) %>% unique()
+
+message("Loading Samples")
+input_table = fread(args$input_table, header = T) %>% arrange(patient, sample_id)
+for (i in 1:nrow(input_table)){
+  sample = input_table$sample_id[i]
+  genome_build = input_table$genome_build[i]
+  print(genome_build)
+  if (tolower(genome_build) %notin% c("hg19","grch37","hg38","grch38")){
+    stop(paste0("Genome build not recognized: ", genome_build, ". Must be in the following list: hg19, hg38, grch37, grch38 (case will be ignored)."))
+  }
+  file = input_table$fp_tsv[i]
+  if (!file.exists(file)){
+    stop(paste0("File does not exist: ", input_table$fp_tsv[i]))
+  }
+  temp_dataset <- fread(file, header = T, sep="\t")
+  colnames(temp_dataset) = c("Locus", "Count", "Genotype","VAF")
+  temp_dataset = separate(temp_dataset, Count, into = c(NA,'DP1',NA,'DP2'), remove = F)
+  temp_dataset$DP2[is.na(temp_dataset$DP2)==T] <- 0
+  temp_dataset$DP = as.numeric(temp_dataset$DP1) + as.numeric(temp_dataset$DP2)
+  temp_dataset = temp_dataset[temp_dataset$DP >= args$depth_filter,] ## keeping loci >= 20 dp by default
+  temp_dataset$VAF[is.na(temp_dataset$VAF)==T] <- 0
+  #temp_dataset$Sample = sample #only loci with DP >= depth filter will have Sample info
+  temp_dataset$Sample <- rep(sample, nrow(temp_dataset))
+  temp_dataset = temp_dataset %>% select("Locus","Genotype","Sample","VAF")
+  temp_dataset$Locus = str_replace(temp_dataset$Locus,"chr","")
+
+  if (tolower(genome_build) %in% c("hg19","grch37")){
+    temp_dataset = merge(hg19_hg38_mapper, temp_dataset, by.x = "Loci_hg19", by.y = "Locus", all.x = T)
+    temp_dataset$VAF[is.na(temp_dataset$VAF)==T] <- 0
+  } else if (tolower(genome_build) %in% c("hg38","grch38")){
+    temp_dataset = merge(hg19_hg38_mapper, temp_dataset, by.x = "Loci_hg38", by.y = "Locus", all.x = T)
+    temp_dataset$VAF[is.na(temp_dataset$VAF)==T] <- 0
+  }
+
+  if (!exists("all_gbcm")){
+    all_gbcm = temp_dataset
+  } else {
+    all_gbcm = rbind(all_gbcm, temp_dataset)
+  }
+}
+all_gbcm = all_gbcm[is.na(all_gbcm$Sample)==F,] # filters out loci that don't have Sample info (i.e. loci not passing DP filter)
+all_gbcm$VAF = round(as.numeric(all_gbcm$VAF), 5)
+
+wide_all_gbcm = all_gbcm %>% pivot_wider(names_from = Sample, values_from = c(Genotype, VAF))
+
+message("Creating final GBCM file")
+
+all_fp_gbcm_final = merge(hg19_hg38_mapper, wide_all_gbcm,all.x = T)
+
+if (!dir.exists(args$analysis_folder)) {
+  dir.create(args$analysis_folder, recursive = TRUE)
+} else {
+  print(paste("Directory already exists:", args$analysis_folder))
+}
+
+message(paste("Output file: ", args$analysis_folder,"/",args$depth_filter,"DPfilter_ALL_FP.txt", sep=""))
+
+all_fp_gbcm_final <- apply(all_fp_gbcm_final,2,as.character)
+write.table(all_fp_gbcm_final, file = paste(args$analysis_folder,"/",args$depth_filter,"DPfilter_ALL_FP.txt", sep=""), append = F, sep = "\t", row.names = F, quote = F)
+
+message("FP file completed")

modules/msk/custom/fingerprintcombine/tests/loci_mapping.tsv

@@ -0,0 +1,10 @@
+GRCH37_CHROM	GRCH37_POS	GRCH38_CHROM	GRCH38_POS
+MT192765.1	197	MT192765.1	199
+MT192765.1	4788	MT192765.1	4900
+MT192765.1	8236	MT192765.1	8257
+MT192765.1	10506	MT192765.1	10528
+MT192765.1	11037	MT192765.1	11059
+MT192765.1	15009	MT192765.1	15500
+MT192765.1	18807	MT192765.1	18929
+MT192765.1	23813	MT192765.1	24835
+MT192765.1	24103	MT192765.1	25125

modules/msk/custom/fingerprintcombine/tests/main.nf.test

@@ -0,0 +1,105 @@
+// nf-core modules test custom/fingerprintcombine
+nextflow_process {
+
+    name "Test Process CUSTOM_FINGERPRINTCOMBINE"
+    script "../main.nf"
+    process "CUSTOM_FINGERPRINTCOMBINE"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_msk"
+    tag "custom"
+    tag "custom/fingerprintcombine"
+    tag "gbcms"
+    tag "custom/fingerprintvcfparser"
+
+    test("sarscov2 - bam") {
+
+        setup {
+            run("GBCMS"){
+                script "../../../gbcms/main.nf"
+                process {
+                    """
+                    input[0] = Channel.of(
+                                [
+                                    [ id:'test', sample:'test', pool:'mypool' ], // meta map
+                                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+                                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
+                                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                                    "variant_file.vcf"
+                                ],
+                                [
+                                    [ id:'test2', sample:'test2', pool:'mypool' ], // meta map
+                                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
+                                    file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true),
+                                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true),
+                                    "variant_file.vcf"
+                                ],
+                    )
+                    input[1] = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    input[2] = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+                    """
+                }
+            }
+            run("CUSTOM_FINGERPRINTVCFPARSER"){
+                script "../../fingerprintvcfparser/main.nf"
+                process {
+                    """
+                    input[0] = GBCMS.out.variant_file
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = CUSTOM_FINGERPRINTVCFPARSER.out.tsv
+                    .map{ meta, tsv ->
+                        println meta
+                        [[id:meta.pool], tsv, meta.id, "hg19","default"]
+                    }.groupTuple(by:[0])
+                input[1] = file("$baseDir/modules/msk/custom/fingerprintcombine/tests/loci_mapping.tsv", checkIfExists:true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [id:"testsample"],
+                    [file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)],
+                    ["testsample"],
+                    ["hg19"],
+                    ["default"]
+                 ]
+                input[1] = file("$baseDir/modules/msk/custom/fingerprintcombine/tests/loci_mapping.tsv", checkIfExists:true)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}