From 2187c417de21b24c6a4c460048e52c7c26feeef7 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Thu, 29 Jun 2023 17:27:10 -0700
Subject: [PATCH 01/16] add r-script and docker

---
 config/default.config         |  4 +++
 metadata.yaml                 |  1 +
 module/intersect-processes.nf | 32 ++++++++++++++++++++---
 module/intersect.nf           |  7 +++++
 r-scripts/plot-intersect.R    | 48 +++++++++++++++++++++++++++++++++++
 5 files changed, 89 insertions(+), 3 deletions(-)
 create mode 100644 r-scripts/plot-intersect.R

diff --git a/config/default.config b/config/default.config
index 0f732270..77c03041 100644
--- a/config/default.config
+++ b/config/default.config
@@ -23,6 +23,7 @@ params {
     manta_version = "1.6.0"
     MuSE_version = "2.0"
     BCFtools_version = "1.17"
+    call_ssnv_r_version = "${manifest.version}"
     docker_image_samtools = "${-> params.docker_container_registry}/samtools:${params.samtools_version}"
     docker_image_validate_params = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
     docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}"
@@ -32,6 +33,9 @@ params {
     docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}"
     docker_image_MuSE = "${-> params.docker_container_registry}/muse:${params.MuSE_version}"
     docker_image_BCFtools = "${-> params.docker_container_registry}/bcftools:${params.BCFtools_version}"
+    docker_image_r_scripts = "${-> params.docker_container_registry}/call-ssnv-r:${params.call_ssnv_r_version}"
+    "
+
 
 }
 
diff --git a/metadata.yaml b/metadata.yaml
index aea10576..34d89290 100644
--- a/metadata.yaml
+++ b/metadata.yaml
@@ -6,3 +6,4 @@ Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel F
 Languages: ['Docker', 'Nextflow']
 Dependencies: ['Docker', 'Nextflow']
 Tools: ['GATK 4.4.0.0', 'SomaticSniper v1.0.5.0', 'SAMtools v1.16.1', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0', BCFtools v1.17]
+image_name: 'call-ssnv-r'
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 7bf8696d..f9c8794b 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -4,7 +4,8 @@ log.info """\
 ====================================
 Docker Images:
 - docker_image_BCFtools: ${params.docker_image_BCFtools}
-
+- docker_image_r_scripts: ${params.docker_image_r_scripts}
+====================================
 """
 process intersect_VCFs_BCFtools {
     container params.docker_image_BCFtools
@@ -33,8 +34,7 @@ process intersect_VCFs_BCFtools {
     path "*.vcf.gz.tbi", emit: consensus_idx
     path ".command.*"
     path "isec-2-or-more"
-    path "isec-1-or-more/sites.txt"
-    path "isec-1-or-more/README.txt"
+    path "isec-1-or-more" emit: isec_dir
 
     script:
     vcf_list = vcfs.join(' ')
@@ -45,3 +45,29 @@ process intersect_VCFs_BCFtools {
     bcftools isec --output-type z --prefix isec-1-or-more --regions-file ${call_region} ${vcf_list}
     """
     }
+
+
+process plot_venn_R
+    container params.docker_image_r_scripts
+    publishDir path: "${params.workflow_output_dir}/output",
+        mode: "copy",
+        pattern: "*.tiff"
+    publishDir path: "${params.workflow_log_output_dir}",
+        mode: "copy",
+        pattern: ".command.*",
+        saveAs: { "${task.process.replace(':', '/')}-${task.index}/log${file(it).getName()}" }
+
+    input:
+    path isec_dir
+    path script_dir
+
+    output:
+    path ".command.*"
+    path "*.tiff"
+
+    script:
+    """
+    set -euo pipefail
+    Rscript ${script_dir}/plot_venn.R --isec_dir ${isec_dir} --dataset params.dataset_id
+    """
+    }
diff --git a/module/intersect.nf b/module/intersect.nf
index 2e99f7a5..ce2fd046 100644
--- a/module/intersect.nf
+++ b/module/intersect.nf
@@ -2,6 +2,9 @@ include { generate_sha512sum } from './common'
 include { intersect_VCFs_BCFtools } from './intersect-processes.nf'
 
 workflow intersect {
+    // pass bin directory in project folder as channel into docker
+    script_dir_ch = Channel.fromPath("$projectDir/r-scripts", checkIfExists: true)
+
     take:
     tool_vcfs
     tool_indices
@@ -21,4 +24,8 @@ workflow intersect {
                 .map{ it -> ["${file(it).getName().split('_')[0]}-SNV-idx", it]}
                 )
         generate_sha512sum(file_for_sha512)
+        plot_venn_R(
+            intersect_VCFs_BCFtools.out.isec_dir,
+            script_dir_ch
+        )
     }
diff --git a/r-scripts/plot-intersect.R b/r-scripts/plot-intersect.R
new file mode 100644
index 00000000..1537a5b7
--- /dev/null
+++ b/r-scripts/plot-intersect.R
@@ -0,0 +1,48 @@
+# Script to plot the Venn diagram of the intersection of the VCF files
+# Initial commit: Sorel Fitz-Gibbon 2023-06-29
+
+## 1. Setup the environment ########################################################################
+library('argparse');
+library('BoutrosLab.utilities');
+library('VennDiagram');
+
+# tmp: for testing
+#args <- list();
+#args$path <- '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-intersect-vcfs/call-sSNV-6.0.0/CPCG0000000196-T001-P01'
+#args$valid_algorithm <- 'NULL';
+#args$dataset.id <- 'CPCG';
+#args$output.dir <- paste(getwd(), paste(gsub(' |:', '-', Sys.time()), 'VCF-Comparison-Result', sep = '_'), sep = '/');
+
+## 2. Parse the arguments ##########################################################################
+parser <- ArgumentParser();
+parser$add_argument('-i', '--isec_dir', help = 'The directory containing the output from BCFtools intersect', type = 'character');
+parser$add_argument('-d', '--dataset', help = 'The dataset ID passed from nextflow', type = 'character');
+args <- parser$parse_args();
+
+### Main ##########################################################
+algorithms <- readLines(paste0(args$isec_dir,'/README.txt'));
+algorithms <- algorithms[grep(paste0('^', args$isec_dir), algorithms)];
+algorithms <- gsub(paste0(args$isec_dir,'.*\t'), '', algorithms);
+algorithms <- gsub('-.*', '', algorithms);
+sites <- read.table(paste0(args$isec_dir,'/sites.txt'), header = FALSE, colClasses = 'character');
+split_col <- strsplit(as.character(sites$V5), "");
+sites$col1 <- sapply(split_col, "[", 1);
+sites$col2 <- sapply(split_col, "[", 2);
+sites$col3 <- sapply(split_col, "[", 3);
+sites$col4 <- sapply(split_col, "[", 4);
+sites$V5 <- NULL;
+header <- c('chrom', 'pos', 'ref', 'alt', algorithms);
+colnames(sites) <- header
+variants <- paste(sites$chrom, sites$pos, sep = '_');
+tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1])
+tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)]
+
+VennDiagram::venn.diagram(
+    tool.variants.ordered,
+    filename = generate.filename(args$dataset, 'Venn-diagram', 'tiff' ),
+    fill = c("orange", "red", "green", "blue"),
+    lty = "dashed",
+    cex = 1,
+    cat.cex = 0.8,
+    cat.col = 'black'
+    );

From bd020d324be75f3d312db2c6827369812f64c733 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Fri, 30 Jun 2023 08:03:30 -0700
Subject: [PATCH 02/16] add Dockerfile

---
 Dockerfile | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)
 create mode 100644 Dockerfile

diff --git a/Dockerfile b/Dockerfile
new file mode 100644
index 00000000..ef5fc836
--- /dev/null
+++ b/Dockerfile
@@ -0,0 +1,30 @@
+ARG MINIFORGE_VERSION=22.9.0-2
+ARG UBUNTU_VERSION=20.04
+
+FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
+
+RUN mamba create -qy -p /usr/local \
+        'r-base>=4.2.1' \
+        # R packages
+        r-argparse \
+        r-VennDiagram
+
+# Copy from builder into final image
+FROM ubuntu:${UBUNTU_VERSION} AS final
+COPY --from=builder /usr/local /usr/local
+
+# Add a new user/group called bldocker
+RUN groupadd -g 500001 bldocker \
+    && useradd -r -u 500001 -g bldocker bldocker
+
+WORKDIR /usr/src
+# where's a better place to get this package?
+COPY r-scripts/BoutrosLab.utilities_1.9.10.tar.gz /usr/src
+RUN R -e "install.packages('BoutrosLab.utilities_1.9.10.tar.gz', repos = NULL, type = 'source')"
+RUN rm BoutrosLab.utilities_1.9.10.tar.gz
+
+# Change the default user to bldocker from root
+USER bldocker
+
+LABEL maintainer="Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>"
+LABEL org.opencontainers.image.source=https://github.com/uclahs-cds/call-ssnv-r

From 82ec5d210b183d3bea64c067d36dbaba65b0b15c Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Fri, 30 Jun 2023 13:02:48 -0700
Subject: [PATCH 03/16] debugging

---
 r-scripts/plot-venn.R | 48 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 48 insertions(+)
 create mode 100644 r-scripts/plot-venn.R

diff --git a/r-scripts/plot-venn.R b/r-scripts/plot-venn.R
new file mode 100644
index 00000000..1537a5b7
--- /dev/null
+++ b/r-scripts/plot-venn.R
@@ -0,0 +1,48 @@
+# Script to plot the Venn diagram of the intersection of the VCF files
+# Initial commit: Sorel Fitz-Gibbon 2023-06-29
+
+## 1. Setup the environment ########################################################################
+library('argparse');
+library('BoutrosLab.utilities');
+library('VennDiagram');
+
+# tmp: for testing
+#args <- list();
+#args$path <- '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-intersect-vcfs/call-sSNV-6.0.0/CPCG0000000196-T001-P01'
+#args$valid_algorithm <- 'NULL';
+#args$dataset.id <- 'CPCG';
+#args$output.dir <- paste(getwd(), paste(gsub(' |:', '-', Sys.time()), 'VCF-Comparison-Result', sep = '_'), sep = '/');
+
+## 2. Parse the arguments ##########################################################################
+parser <- ArgumentParser();
+parser$add_argument('-i', '--isec_dir', help = 'The directory containing the output from BCFtools intersect', type = 'character');
+parser$add_argument('-d', '--dataset', help = 'The dataset ID passed from nextflow', type = 'character');
+args <- parser$parse_args();
+
+### Main ##########################################################
+algorithms <- readLines(paste0(args$isec_dir,'/README.txt'));
+algorithms <- algorithms[grep(paste0('^', args$isec_dir), algorithms)];
+algorithms <- gsub(paste0(args$isec_dir,'.*\t'), '', algorithms);
+algorithms <- gsub('-.*', '', algorithms);
+sites <- read.table(paste0(args$isec_dir,'/sites.txt'), header = FALSE, colClasses = 'character');
+split_col <- strsplit(as.character(sites$V5), "");
+sites$col1 <- sapply(split_col, "[", 1);
+sites$col2 <- sapply(split_col, "[", 2);
+sites$col3 <- sapply(split_col, "[", 3);
+sites$col4 <- sapply(split_col, "[", 4);
+sites$V5 <- NULL;
+header <- c('chrom', 'pos', 'ref', 'alt', algorithms);
+colnames(sites) <- header
+variants <- paste(sites$chrom, sites$pos, sep = '_');
+tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1])
+tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)]
+
+VennDiagram::venn.diagram(
+    tool.variants.ordered,
+    filename = generate.filename(args$dataset, 'Venn-diagram', 'tiff' ),
+    fill = c("orange", "red", "green", "blue"),
+    lty = "dashed",
+    cex = 1,
+    cat.cex = 0.8,
+    cat.col = 'black'
+    );

From accf0d6ee89d58428b3464758616e47b0c37ebe1 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Fri, 30 Jun 2023 13:04:01 -0700
Subject: [PATCH 04/16] debugging

---
 Dockerfile                    |  3 +--
 config/default.config         |  1 -
 module/intersect-processes.nf |  4 +--
 r-scripts/plot-intersect.R    | 48 -----------------------------------
 4 files changed, 3 insertions(+), 53 deletions(-)
 delete mode 100644 r-scripts/plot-intersect.R

diff --git a/Dockerfile b/Dockerfile
index ef5fc836..804e72b2 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,11 +17,10 @@ COPY --from=builder /usr/local /usr/local
 RUN groupadd -g 500001 bldocker \
     && useradd -r -u 500001 -g bldocker bldocker
 
-WORKDIR /usr/src
 # where's a better place to get this package?
 COPY r-scripts/BoutrosLab.utilities_1.9.10.tar.gz /usr/src
 RUN R -e "install.packages('BoutrosLab.utilities_1.9.10.tar.gz', repos = NULL, type = 'source')"
-RUN rm BoutrosLab.utilities_1.9.10.tar.gz
+# RUN rm BoutrosLab.utilities_1.9.10.tar.gz
 
 # Change the default user to bldocker from root
 USER bldocker
diff --git a/config/default.config b/config/default.config
index 77c03041..00313b9b 100644
--- a/config/default.config
+++ b/config/default.config
@@ -34,7 +34,6 @@ params {
     docker_image_MuSE = "${-> params.docker_container_registry}/muse:${params.MuSE_version}"
     docker_image_BCFtools = "${-> params.docker_container_registry}/bcftools:${params.BCFtools_version}"
     docker_image_r_scripts = "${-> params.docker_container_registry}/call-ssnv-r:${params.call_ssnv_r_version}"
-    "
 
 
 }
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index f9c8794b..26429064 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -48,7 +48,7 @@ process intersect_VCFs_BCFtools {
 
 
 process plot_venn_R
-    container params.docker_image_r_scripts
+    container test-rvenn
     publishDir path: "${params.workflow_output_dir}/output",
         mode: "copy",
         pattern: "*.tiff"
@@ -68,6 +68,6 @@ process plot_venn_R
     script:
     """
     set -euo pipefail
-    Rscript ${script_dir}/plot_venn.R --isec_dir ${isec_dir} --dataset params.dataset_id
+    Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --dataset params.dataset_id
     """
     }
diff --git a/r-scripts/plot-intersect.R b/r-scripts/plot-intersect.R
deleted file mode 100644
index 1537a5b7..00000000
--- a/r-scripts/plot-intersect.R
+++ /dev/null
@@ -1,48 +0,0 @@
-# Script to plot the Venn diagram of the intersection of the VCF files
-# Initial commit: Sorel Fitz-Gibbon 2023-06-29
-
-## 1. Setup the environment ########################################################################
-library('argparse');
-library('BoutrosLab.utilities');
-library('VennDiagram');
-
-# tmp: for testing
-#args <- list();
-#args$path <- '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-intersect-vcfs/call-sSNV-6.0.0/CPCG0000000196-T001-P01'
-#args$valid_algorithm <- 'NULL';
-#args$dataset.id <- 'CPCG';
-#args$output.dir <- paste(getwd(), paste(gsub(' |:', '-', Sys.time()), 'VCF-Comparison-Result', sep = '_'), sep = '/');
-
-## 2. Parse the arguments ##########################################################################
-parser <- ArgumentParser();
-parser$add_argument('-i', '--isec_dir', help = 'The directory containing the output from BCFtools intersect', type = 'character');
-parser$add_argument('-d', '--dataset', help = 'The dataset ID passed from nextflow', type = 'character');
-args <- parser$parse_args();
-
-### Main ##########################################################
-algorithms <- readLines(paste0(args$isec_dir,'/README.txt'));
-algorithms <- algorithms[grep(paste0('^', args$isec_dir), algorithms)];
-algorithms <- gsub(paste0(args$isec_dir,'.*\t'), '', algorithms);
-algorithms <- gsub('-.*', '', algorithms);
-sites <- read.table(paste0(args$isec_dir,'/sites.txt'), header = FALSE, colClasses = 'character');
-split_col <- strsplit(as.character(sites$V5), "");
-sites$col1 <- sapply(split_col, "[", 1);
-sites$col2 <- sapply(split_col, "[", 2);
-sites$col3 <- sapply(split_col, "[", 3);
-sites$col4 <- sapply(split_col, "[", 4);
-sites$V5 <- NULL;
-header <- c('chrom', 'pos', 'ref', 'alt', algorithms);
-colnames(sites) <- header
-variants <- paste(sites$chrom, sites$pos, sep = '_');
-tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1])
-tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)]
-
-VennDiagram::venn.diagram(
-    tool.variants.ordered,
-    filename = generate.filename(args$dataset, 'Venn-diagram', 'tiff' ),
-    fill = c("orange", "red", "green", "blue"),
-    lty = "dashed",
-    cex = 1,
-    cat.cex = 0.8,
-    cat.col = 'black'
-    );

From b1d6f5feb20a3b765e49d5a346fe8e61ef544d56 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Fri, 30 Jun 2023 14:59:52 -0700
Subject: [PATCH 05/16] lintr errors

---
 r-scripts/plot-venn.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/r-scripts/plot-venn.R b/r-scripts/plot-venn.R
index 1537a5b7..464838fc 100644
--- a/r-scripts/plot-venn.R
+++ b/r-scripts/plot-venn.R
@@ -25,11 +25,11 @@ algorithms <- algorithms[grep(paste0('^', args$isec_dir), algorithms)];
 algorithms <- gsub(paste0(args$isec_dir,'.*\t'), '', algorithms);
 algorithms <- gsub('-.*', '', algorithms);
 sites <- read.table(paste0(args$isec_dir,'/sites.txt'), header = FALSE, colClasses = 'character');
-split_col <- strsplit(as.character(sites$V5), "");
-sites$col1 <- sapply(split_col, "[", 1);
-sites$col2 <- sapply(split_col, "[", 2);
-sites$col3 <- sapply(split_col, "[", 3);
-sites$col4 <- sapply(split_col, "[", 4);
+split.col <- strsplit(as.character(sites$V5), '');
+sites$col1 <- sapply(split.col, '[', 1);
+sites$col2 <- sapply(split.col, '[', 2);
+sites$col3 <- sapply(split.col, '[', 3);
+sites$col4 <- sapply(split.col, '[', 4);
 sites$V5 <- NULL;
 header <- c('chrom', 'pos', 'ref', 'alt', algorithms);
 colnames(sites) <- header
@@ -40,8 +40,8 @@ tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing
 VennDiagram::venn.diagram(
     tool.variants.ordered,
     filename = generate.filename(args$dataset, 'Venn-diagram', 'tiff' ),
-    fill = c("orange", "red", "green", "blue"),
-    lty = "dashed",
+    fill = c('orange', 'red', 'green', 'blue'),
+    lty = 'dashed',
     cex = 1,
     cat.cex = 0.8,
     cat.col = 'black'

From 86e1af52c11f05c9fa86b6d758145500c46450c5 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Fri, 30 Jun 2023 17:41:43 -0700
Subject: [PATCH 06/16] debug

---
 config/default.config               | 4 ++--
 module/intersect-processes.nf       | 7 +++----
 module/intersect.nf                 | 2 +-
 test/config/a_mini-all-tools.config | 1 -
 4 files changed, 6 insertions(+), 8 deletions(-)

diff --git a/config/default.config b/config/default.config
index 00313b9b..852b7b36 100644
--- a/config/default.config
+++ b/config/default.config
@@ -23,7 +23,7 @@ params {
     manta_version = "1.6.0"
     MuSE_version = "2.0"
     BCFtools_version = "1.17"
-    call_ssnv_r_version = "${manifest.version}"
+    call_ssnv_r_version = "${->workflow.manifest.version}"
     docker_image_samtools = "${-> params.docker_container_registry}/samtools:${params.samtools_version}"
     docker_image_validate_params = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
     docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}"
@@ -33,7 +33,7 @@ params {
     docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}"
     docker_image_MuSE = "${-> params.docker_container_registry}/muse:${params.MuSE_version}"
     docker_image_BCFtools = "${-> params.docker_container_registry}/bcftools:${params.BCFtools_version}"
-    docker_image_r_scripts = "${-> params.docker_container_registry}/call-ssnv-r:${params.call_ssnv_r_version}"
+    docker_image_r_scripts = "${-> params.docker_container_registry}/call-ssnv-r:${->params.call_ssnv_r_version}"
 
 
 }
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 26429064..1308030a 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -34,7 +34,7 @@ process intersect_VCFs_BCFtools {
     path "*.vcf.gz.tbi", emit: consensus_idx
     path ".command.*"
     path "isec-2-or-more"
-    path "isec-1-or-more" emit: isec_dir
+    path "isec-1-or-more", emit: isec_dir
 
     script:
     vcf_list = vcfs.join(' ')
@@ -46,9 +46,8 @@ process intersect_VCFs_BCFtools {
     """
     }
 
-
-process plot_venn_R
-    container test-rvenn
+process plot_venn_R {
+    container 'test-rvenn'
     publishDir path: "${params.workflow_output_dir}/output",
         mode: "copy",
         pattern: "*.tiff"
diff --git a/module/intersect.nf b/module/intersect.nf
index ce2fd046..1d5b016f 100644
--- a/module/intersect.nf
+++ b/module/intersect.nf
@@ -1,5 +1,5 @@
 include { generate_sha512sum } from './common'
-include { intersect_VCFs_BCFtools } from './intersect-processes.nf'
+include { intersect_VCFs_BCFtools; plot_venn_R } from './intersect-processes.nf'
 
 workflow intersect {
     // pass bin directory in project folder as channel into docker
diff --git a/test/config/a_mini-all-tools.config b/test/config/a_mini-all-tools.config
index 60d71945..ed70c7b6 100644
--- a/test/config/a_mini-all-tools.config
+++ b/test/config/a_mini-all-tools.config
@@ -38,5 +38,4 @@ params {
     // MuSE options
     dbSNP = '/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
 }
-
 methods.setup()

From dd08db6db6ae95f91d617c783079185506fd4261 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Sat, 1 Jul 2023 15:05:51 -0700
Subject: [PATCH 07/16] minor edits

---
 Dockerfile            | 2 +-
 r-scripts/plot-venn.R | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 804e72b2..3a32673b 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,7 +17,7 @@ COPY --from=builder /usr/local /usr/local
 RUN groupadd -g 500001 bldocker \
     && useradd -r -u 500001 -g bldocker bldocker
 
-# where's a better place to get this package?
+# BoutrosLab.utilities_1.9.10.tar.gz is soft-linked to /hot/resource/R-package/Bout...gz
 COPY r-scripts/BoutrosLab.utilities_1.9.10.tar.gz /usr/src
 RUN R -e "install.packages('BoutrosLab.utilities_1.9.10.tar.gz', repos = NULL, type = 'source')"
 # RUN rm BoutrosLab.utilities_1.9.10.tar.gz
diff --git a/r-scripts/plot-venn.R b/r-scripts/plot-venn.R
index 464838fc..bfb87186 100644
--- a/r-scripts/plot-venn.R
+++ b/r-scripts/plot-venn.R
@@ -1,5 +1,10 @@
 # Script to plot the Venn diagram of the intersection of the VCF files
 # Initial commit: Sorel Fitz-Gibbon 2023-06-29
+# Input:
+#  -i, --isec_dir: The directory containing the output from BCFtools intersect
+#  -d, --dataset: The dataset ID passed from nextflow
+# Output:
+# - A Venn diagram of the intersection of the VCF files
 
 ## 1. Setup the environment ########################################################################
 library('argparse');

From 58fd8b04f7e00f45e1fa2fc9d5ef27144137196e Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Mon, 3 Jul 2023 15:07:14 -0700
Subject: [PATCH 08/16] docker call-ssnv-r integrated

---
 Dockerfile                    | 2 +-
 module/intersect-processes.nf | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 3a32673b..54c3884d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -19,7 +19,7 @@ RUN groupadd -g 500001 bldocker \
 
 # BoutrosLab.utilities_1.9.10.tar.gz is soft-linked to /hot/resource/R-package/Bout...gz
 COPY r-scripts/BoutrosLab.utilities_1.9.10.tar.gz /usr/src
-RUN R -e "install.packages('BoutrosLab.utilities_1.9.10.tar.gz', repos = NULL, type = 'source')"
+RUN R -e "install.packages('/usr/src/BoutrosLab.utilities_1.9.10.tar.gz', repos = NULL, type = 'source')"
 # RUN rm BoutrosLab.utilities_1.9.10.tar.gz
 
 # Change the default user to bldocker from root
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 1308030a..8230b522 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -47,7 +47,7 @@ process intersect_VCFs_BCFtools {
     }
 
 process plot_venn_R {
-    container 'test-rvenn'
+    container params.docker_image_r_scripts
     publishDir path: "${params.workflow_output_dir}/output",
         mode: "copy",
         pattern: "*.tiff"

From cc603878df0a264bff66b344862be4f066d28da9 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Fri, 7 Jul 2023 11:49:36 -0700
Subject: [PATCH 09/16] add regions to plot script and start per chr QC

---
 config/default.config         |  2 +-
 module/intersect-processes.nf |  5 ++--
 module/intersect.nf           |  3 ++-
 r-scripts/plot-venn.R         | 50 +++++++++++++++++++++++------------
 4 files changed, 39 insertions(+), 21 deletions(-)

diff --git a/config/default.config b/config/default.config
index 852b7b36..f90d4bb1 100644
--- a/config/default.config
+++ b/config/default.config
@@ -23,7 +23,7 @@ params {
     manta_version = "1.6.0"
     MuSE_version = "2.0"
     BCFtools_version = "1.17"
-    call_ssnv_r_version = "${->workflow.manifest.version}"
+    call_ssnv_r_version = "dev"
     docker_image_samtools = "${-> params.docker_container_registry}/samtools:${params.samtools_version}"
     docker_image_validate_params = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
     docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}"
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 8230b522..c150addd 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -57,8 +57,9 @@ process plot_venn_R {
         saveAs: { "${task.process.replace(':', '/')}-${task.index}/log${file(it).getName()}" }
 
     input:
-    path isec_dir
     path script_dir
+    path isec_dir
+    path call_region
 
     output:
     path ".command.*"
@@ -67,6 +68,6 @@ process plot_venn_R {
     script:
     """
     set -euo pipefail
-    Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --dataset params.dataset_id
+    Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --dataset ${params.dataset_id} --regions ${params.call_region}
     """
     }
diff --git a/module/intersect.nf b/module/intersect.nf
index 1d5b016f..1b8238f9 100644
--- a/module/intersect.nf
+++ b/module/intersect.nf
@@ -25,7 +25,8 @@ workflow intersect {
                 )
         generate_sha512sum(file_for_sha512)
         plot_venn_R(
+            script_dir_ch,
             intersect_VCFs_BCFtools.out.isec_dir,
-            script_dir_ch
+            params.call_region
         )
     }
diff --git a/r-scripts/plot-venn.R b/r-scripts/plot-venn.R
index bfb87186..55264366 100644
--- a/r-scripts/plot-venn.R
+++ b/r-scripts/plot-venn.R
@@ -3,28 +3,42 @@
 # Input:
 #  -i, --isec_dir: The directory containing the output from BCFtools intersect
 #  -d, --dataset: The dataset ID passed from nextflow
+#  -r, --regions: call regions (for single chromosome QC plotting)
 # Output:
 # - A Venn diagram of the intersection of the VCF files
 
-## 1. Setup the environment ########################################################################
+## Setup the environment ###########################################################################
 library('argparse');
 library('BoutrosLab.utilities');
 library('VennDiagram');
 
 # tmp: for testing
 #args <- list();
-#args$path <- '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-intersect-vcfs/call-sSNV-6.0.0/CPCG0000000196-T001-P01'
-#args$valid_algorithm <- 'NULL';
-#args$dataset.id <- 'CPCG';
-#args$output.dir <- paste(getwd(), paste(gsub(' |:', '-', Sys.time()), 'VCF-Comparison-Result', sep = '_'), sep = '/');
+#args$isec_dir <- 'isec-1-or-more';
+#args$dataset<- 'CPCG';
+#args$regions_file <- '/hot/ref/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz';
 
-## 2. Parse the arguments ##########################################################################
+## Parse the arguments #############################################################################
 parser <- ArgumentParser();
 parser$add_argument('-i', '--isec_dir', help = 'The directory containing the output from BCFtools intersect', type = 'character');
 parser$add_argument('-d', '--dataset', help = 'The dataset ID passed from nextflow', type = 'character');
+parser$add_argument('-r', '--regions', help = 'call regions (for single chromosome QC plotting)', type = 'character');
 args <- parser$parse_args();
 
-### Main ##########################################################
+## Function: plot venn diagram #####################################################################
+plot.venn <- function(tool.variants, outfile) {
+    VennDiagram::venn.diagram(
+        tool.variants.ordered,
+        filename = outfile,
+        fill = c('orange', 'red', 'green', 'blue'),
+        lty = 'dashed',
+        cex = 1,
+        cat.cex = 0.8,
+        cat.col = 'black'
+        );
+    }
+
+### Main ###########################################################################################
 algorithms <- readLines(paste0(args$isec_dir,'/README.txt'));
 algorithms <- algorithms[grep(paste0('^', args$isec_dir), algorithms)];
 algorithms <- gsub(paste0(args$isec_dir,'.*\t'), '', algorithms);
@@ -40,14 +54,16 @@ header <- c('chrom', 'pos', 'ref', 'alt', algorithms);
 colnames(sites) <- header
 variants <- paste(sites$chrom, sites$pos, sep = '_');
 tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1])
-tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)]
+tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)];
+plot.venn(tool.variants.ordered, generate.filename(args$dataset, 'Venn-diagram', 'tiff'));
 
-VennDiagram::venn.diagram(
-    tool.variants.ordered,
-    filename = generate.filename(args$dataset, 'Venn-diagram', 'tiff' ),
-    fill = c('orange', 'red', 'green', 'blue'),
-    lty = 'dashed',
-    cex = 1,
-    cat.cex = 0.8,
-    cat.col = 'black'
-    );
+## Single chromosome QC ############################################################################
+regions <- read.table(args$regions, header = FALSE, colClasses = c('character', 'NULL', 'NULL'));
+# keep tools ordered by number of variants in full set
+tool.order <- names(tool.variants.ordered);
+for chr in unique(regions$V1) {
+    chr.sites <- sites[sites$chrom == chr,];
+    chr.variants <- paste(chr.sites$chrom, chr.sites$pos, sep = '_');
+    chr.tool.variants <- lapply(chr.sites[, tool.order], function(x) chr.variants[x == 1])
+    #... heatmap
+    }

From 8450b7f752e18d5081feb246310febba4e9ba816 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Tue, 25 Jul 2023 15:23:50 -0700
Subject: [PATCH 10/16] moving per chr QC to another PR. still need to get
 BoutrosLab.utilities from github

---
 CHANGELOG.md                  |  7 ++----
 config/default.config         |  6 ++---
 module/intersect-processes.nf | 43 +++++++++++++++++------------------
 module/intersect.nf           |  1 -
 r-scripts/plot-venn.R         | 24 +++----------------
 5 files changed, 28 insertions(+), 53 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 41d201da..27b2df33 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [Unreleased]
 
 ### Added
+- Add variant intersection Venn diagram
 - Add regions filter to variant intersections
 - Add second BCFtools step to create full presence/absence variant table (including private)
 - Add workflow to create a `consensus.vcf` that includes SNVs found by two or more variant callers
@@ -14,12 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Add `split_VCF_bcftools` to `Mutect2` workflow, separating SNVs, MNVs and Indels
 
 ### Changed
-- Keep `bam-readcount` output in `SomaticSniper` QC folder
-- reconfigure call_regions to intersect_regions 
-- Update to BCFtools v1.17
-=======
 - reconfigure intersect_regions to use all contigs except `decoy`
-- reconfigure call_regions to intersect_regions 
+- reconfigure call_regions to intersect_regions
 - Update to BCFtools v1.17
 - Keep `bam-readcount` output in `SomaticSniper` QC folder
 - Update `MuSE` to `v2.0.2`
diff --git a/config/default.config b/config/default.config
index cc9d3514..4f3a2d12 100644
--- a/config/default.config
+++ b/config/default.config
@@ -23,6 +23,7 @@ params {
     manta_version = "1.6.0"
     MuSE_version = "2.0.2"
     BCFtools_version = "1.17"
+    call_ssnv_r_version = "dev"
     docker_image_samtools = "${-> params.docker_container_registry}/samtools:${params.samtools_version}"
     docker_image_validate_params = "${-> params.docker_container_registry}/pipeval:${params.pipeval_version}"
     docker_image_GATK = "broadinstitute/gatk:${params.GATK_version}"
@@ -32,9 +33,7 @@ params {
     docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}"
     docker_image_MuSE = "${-> params.docker_container_registry}/muse:${params.MuSE_version}"
     docker_image_BCFtools = "${-> params.docker_container_registry}/bcftools:${params.BCFtools_version}"
-    docker_image_r_scripts = "${-> params.docker_container_registry}/call-ssnv-r:${->params.call_ssnv_r_version}"
-
-
+    docker_image_r_scripts = "${-> params.docker_container_registry}/call-ssnv-r:${params.call_ssnv_r_version}"
 }
 
 docker {
@@ -44,7 +43,6 @@ docker {
     runOptions = "${uid_and_gid} ${all_group_ids}"
 }
 
-
 process {
     executor = 'local'
 }
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 02743757..fb902c1b 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -50,28 +50,27 @@ process intersect_VCFs_BCFtools {
     """
     }
 
-process plot_venn_R {
-    container params.docker_image_r_scripts
-    publishDir path: "${params.workflow_output_dir}/output",
-        mode: "copy",
-        pattern: "*.tiff"
-    publishDir path: "${params.workflow_log_output_dir}",
-        mode: "copy",
-        pattern: ".command.*",
-        saveAs: { "${task.process.replace(':', '/')}-${task.index}/log${file(it).getName()}" }
+ process plot_venn_R {
+     container params.docker_image_r_scripts
+     publishDir path: "${params.workflow_output_dir}/output",
+         mode: "copy",
+         pattern: "*.tiff"
+     publishDir path: "${params.workflow_log_output_dir}",
+         mode: "copy",
+         pattern: ".command.*",
+         saveAs: { "${task.process.replace(':', '/')}-${task.index}/log${file(it).getName()}" }
 
-    input:
-    path script_dir
-    path isec_dir
-    path call_region
+     input:
+     path script_dir
+     path isec_dir
 
-    output:
-    path ".command.*"
-    path "*.tiff"
+     output:
+     path ".command.*"
+     path "*.tiff"
 
-    script:
-    """
-    set -euo pipefail
-    Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --dataset ${params.dataset_id} --regions ${params.call_region}
-    """
-    }
+     script:
+     """
+     set -euo pipefail
+     Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --dataset ${params.dataset_id}
+     """
+     }
diff --git a/module/intersect.nf b/module/intersect.nf
index 4cd90475..c6d0da24 100644
--- a/module/intersect.nf
+++ b/module/intersect.nf
@@ -27,6 +27,5 @@ workflow intersect {
         plot_venn_R(
             script_dir_ch,
             intersect_VCFs_BCFtools.out.isec_dir,
-            params.call_region
         )
     }
diff --git a/r-scripts/plot-venn.R b/r-scripts/plot-venn.R
index 55264366..c51ff605 100644
--- a/r-scripts/plot-venn.R
+++ b/r-scripts/plot-venn.R
@@ -1,28 +1,20 @@
-# Script to plot the Venn diagram of the intersection of the VCF files
+# Script to plot a Venn diagram of shared variants from the different SNV calling algorithms, using the output of BCFtools isec
 # Initial commit: Sorel Fitz-Gibbon 2023-06-29
 # Input:
 #  -i, --isec_dir: The directory containing the output from BCFtools intersect
 #  -d, --dataset: The dataset ID passed from nextflow
-#  -r, --regions: call regions (for single chromosome QC plotting)
 # Output:
-# - A Venn diagram of the intersection of the VCF files
+# - A Venn diagram of shared variant counts from the BCFtools intersection of the VCF files
 
 ## Setup the environment ###########################################################################
 library('argparse');
 library('BoutrosLab.utilities');
 library('VennDiagram');
 
-# tmp: for testing
-#args <- list();
-#args$isec_dir <- 'isec-1-or-more';
-#args$dataset<- 'CPCG';
-#args$regions_file <- '/hot/ref/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz';
-
 ## Parse the arguments #############################################################################
 parser <- ArgumentParser();
 parser$add_argument('-i', '--isec_dir', help = 'The directory containing the output from BCFtools intersect', type = 'character');
 parser$add_argument('-d', '--dataset', help = 'The dataset ID passed from nextflow', type = 'character');
-parser$add_argument('-r', '--regions', help = 'call regions (for single chromosome QC plotting)', type = 'character');
 args <- parser$parse_args();
 
 ## Function: plot venn diagram #####################################################################
@@ -39,6 +31,7 @@ plot.venn <- function(tool.variants, outfile) {
     }
 
 ### Main ###########################################################################################
+# Get intersection counts from BCFtools isec output and format for plotting
 algorithms <- readLines(paste0(args$isec_dir,'/README.txt'));
 algorithms <- algorithms[grep(paste0('^', args$isec_dir), algorithms)];
 algorithms <- gsub(paste0(args$isec_dir,'.*\t'), '', algorithms);
@@ -56,14 +49,3 @@ variants <- paste(sites$chrom, sites$pos, sep = '_');
 tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1])
 tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)];
 plot.venn(tool.variants.ordered, generate.filename(args$dataset, 'Venn-diagram', 'tiff'));
-
-## Single chromosome QC ############################################################################
-regions <- read.table(args$regions, header = FALSE, colClasses = c('character', 'NULL', 'NULL'));
-# keep tools ordered by number of variants in full set
-tool.order <- names(tool.variants.ordered);
-for chr in unique(regions$V1) {
-    chr.sites <- sites[sites$chrom == chr,];
-    chr.variants <- paste(chr.sites$chrom, chr.sites$pos, sep = '_');
-    chr.tool.variants <- lapply(chr.sites[, tool.order], function(x) chr.variants[x == 1])
-    #... heatmap
-    }

From 1e9591819b8fbb632b3ea9602d5c66a43630adfd Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Tue, 1 Aug 2023 08:25:12 -0700
Subject: [PATCH 11/16] still working on Dockerfile

---
 Dockerfile | 36 ++++++++++++++++++++++++++++++++----
 1 file changed, 32 insertions(+), 4 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 54c3884d..99eb9991 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -12,15 +12,43 @@ RUN mamba create -qy -p /usr/local \
 # Copy from builder into final image
 FROM ubuntu:${UBUNTU_VERSION} AS final
 COPY --from=builder /usr/local /usr/local
+ARG DEBIAN_FRONTEND=noninteractive
 
 # Add a new user/group called bldocker
 RUN groupadd -g 500001 bldocker \
     && useradd -r -u 500001 -g bldocker bldocker
 
-# BoutrosLab.utilities_1.9.10.tar.gz is soft-linked to /hot/resource/R-package/Bout...gz
-COPY r-scripts/BoutrosLab.utilities_1.9.10.tar.gz /usr/src
-RUN R -e "install.packages('/usr/src/BoutrosLab.utilities_1.9.10.tar.gz', repos = NULL, type = 'source')"
-# RUN rm BoutrosLab.utilities_1.9.10.tar.gz
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends libxml2 libxml2-dev libcurl4-gnutls-dev build-essential \
+    libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev r-cran-rgl git libssl-dev r-cran-curl && \
+    apt-get clean && rm -rf /var/lib/apt/lists/*
+
+RUN R -q -e 'install.packages("devtools", dependencies = TRUE)' && \
+    R -q -e 'devtools::install_github("uclahs-cds/public-R-BoutrosLab-utilities")'
+## Install required tools to build R packages
+#RUN apt-get update && apt-get install -y \
+#    --no-install-recommends \
+#    build-essential \
+#    libcurl4-gnutls-dev \
+#    libxml2-dev \
+#    libssl-dev \
+
+#
+## Install required tools to build R packages
+#RUN apt-get update && apt-get install -y \
+#    --no-install-recommends \
+#    build-essential \
+#    libcurl4-gnutls-dev \
+#    libxml2-dev \
+#    libssl-dev \
+#    git \
+#
+## Clone BoutrosLab.utilities repository
+#RUN git clone https://github.com/uclahs-cds/public-R-BoutrosLab-utilities.git /usr/src/BoutrosLab.utilities
+#
+## Build and install the package from the cloned repository
+#RUN R CMD build /usr/src/BoutrosLab.utilities
+#RUN R CMD INSTALL /usr/src/BoutrosLab.utilities/BoutrosLab.utilities_*.tar.gz
 
 # Change the default user to bldocker from root
 USER bldocker

From 874f15c92c8003b3e5a6028fe23193eb49688437 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Tue, 1 Aug 2023 16:29:14 -0700
Subject: [PATCH 12/16] fix dockerfile and add comments to main.nf

---
 Dockerfile | 48 ++++++++++--------------------------------------
 main.nf    |  3 +++
 2 files changed, 13 insertions(+), 38 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 99eb9991..bc6f8f86 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,52 +3,24 @@ ARG UBUNTU_VERSION=20.04
 
 FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
 
-RUN mamba create -qy -p /usr/local \
-        'r-base>=4.2.1' \
-        # R packages
-        r-argparse \
-        r-VennDiagram
-
 # Copy from builder into final image
-FROM ubuntu:${UBUNTU_VERSION} AS final
+FROM ubuntu:${UBUNTU_VERSION}
 COPY --from=builder /usr/local /usr/local
-ARG DEBIAN_FRONTEND=noninteractive
 
-# Add a new user/group called bldocker
-RUN groupadd -g 500001 bldocker \
-    && useradd -r -u 500001 -g bldocker bldocker
+ARG DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update && \
-    apt-get install -y --no-install-recommends libxml2 libxml2-dev libcurl4-gnutls-dev build-essential \
+    apt-get install -y --no-install-recommends libxml2 libxml2-dev libcurl4-gnutls-dev build-essential r-base r-base-dev \
     libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev r-cran-rgl git libssl-dev r-cran-curl && \
+    git libssl-dev r-cran-curl && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
-RUN R -q -e 'install.packages("devtools", dependencies = TRUE)' && \
-    R -q -e 'devtools::install_github("uclahs-cds/public-R-BoutrosLab-utilities")'
-## Install required tools to build R packages
-#RUN apt-get update && apt-get install -y \
-#    --no-install-recommends \
-#    build-essential \
-#    libcurl4-gnutls-dev \
-#    libxml2-dev \
-#    libssl-dev \
-
-#
-## Install required tools to build R packages
-#RUN apt-get update && apt-get install -y \
-#    --no-install-recommends \
-#    build-essential \
-#    libcurl4-gnutls-dev \
-#    libxml2-dev \
-#    libssl-dev \
-#    git \
-#
-## Clone BoutrosLab.utilities repository
-#RUN git clone https://github.com/uclahs-cds/public-R-BoutrosLab-utilities.git /usr/src/BoutrosLab.utilities
-#
-## Build and install the package from the cloned repository
-#RUN R CMD build /usr/src/BoutrosLab.utilities
-#RUN R CMD INSTALL /usr/src/BoutrosLab.utilities/BoutrosLab.utilities_*.tar.gz
+RUN R -q -e 'install.packages(c("devtools", "argparse", "VennDiagram"))'
+RUN R -q -e 'devtools::install_github("uclahs-cds/public-R-BoutrosLab-utilities")'
+
+# Add a new user/group called bldocker
+RUN groupadd -g 500001 bldocker \
+    && useradd -r -u 500001 -g bldocker bldocker
 
 # Change the default user to bldocker from root
 USER bldocker
diff --git a/main.nf b/main.nf
index 5b536791..82745a97 100755
--- a/main.nf
+++ b/main.nf
@@ -152,6 +152,7 @@ workflow {
         run_GetSampleName_Mutect2_tumor(tumor_input.tumor_bam)
         }
 
+    // Set empty channels so any unused tools don't cause failure at intersect step
     Channel.empty().set { somaticsniper_vcf_ch }
     Channel.empty().set { strelka2_vcf_ch }
     Channel.empty().set { mutect2_vcf_ch }
@@ -209,6 +210,8 @@ workflow {
             muse.out.vcf.set { muse_vcf_ch }
             muse.out.idx.set { muse_idx_ch }
         }
+
+    // Intersect all vcf files
     if (params.algorithm.size() > 1) {
         tool_vcfs = (somaticsniper_vcf_ch
             .mix(strelka2_vcf_ch)

From 29e4fb381d91b7859052adf62785632d742e220f Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Wed, 2 Aug 2023 11:54:57 -0700
Subject: [PATCH 13/16] move and update Dockerfile

---
 Dockerfile => docker/plot-venn/Dockerfile | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)
 rename Dockerfile => docker/plot-venn/Dockerfile (77%)

diff --git a/Dockerfile b/docker/plot-venn/Dockerfile
similarity index 77%
rename from Dockerfile
rename to docker/plot-venn/Dockerfile
index bc6f8f86..ef47a4a3 100644
--- a/Dockerfile
+++ b/docker/plot-venn/Dockerfile
@@ -1,17 +1,11 @@
-ARG MINIFORGE_VERSION=22.9.0-2
 ARG UBUNTU_VERSION=20.04
-
-FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
-
-# Copy from builder into final image
 FROM ubuntu:${UBUNTU_VERSION}
-COPY --from=builder /usr/local /usr/local
 
 ARG DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends libxml2 libxml2-dev libcurl4-gnutls-dev build-essential r-base r-base-dev \
-    libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev r-cran-rgl git libssl-dev r-cran-curl && \
+    libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev r-cran-rgl \
     git libssl-dev r-cran-curl && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 

From 887ab0b3e8af1249fd91617f56bb902061267b8e Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Wed, 2 Aug 2023 11:57:13 -0700
Subject: [PATCH 14/16] update docker image parameter name

---
 config/default.config         | 2 +-
 module/intersect-processes.nf | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/config/default.config b/config/default.config
index 4f3a2d12..01b47390 100644
--- a/config/default.config
+++ b/config/default.config
@@ -33,7 +33,7 @@ params {
     docker_image_manta = "${-> params.docker_container_registry}/manta:${params.manta_version}"
     docker_image_MuSE = "${-> params.docker_container_registry}/muse:${params.MuSE_version}"
     docker_image_BCFtools = "${-> params.docker_container_registry}/bcftools:${params.BCFtools_version}"
-    docker_image_r_scripts = "${-> params.docker_container_registry}/call-ssnv-r:${params.call_ssnv_r_version}"
+    docker_image_r_VennDiagram = "${-> params.docker_container_registry}/call-ssnv-r:${params.call_ssnv_r_version}"
 }
 
 docker {
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index fb902c1b..d5f5b700 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -4,7 +4,7 @@ log.info """\
 ====================================
 Docker Images:
 - docker_image_BCFtools: ${params.docker_image_BCFtools}
-- docker_image_r_scripts: ${params.docker_image_r_scripts}
+- docker_image_r_scripts: ${params.docker_image_r_VennDiagram}
 ====================================
 """
 process intersect_VCFs_BCFtools {
@@ -51,7 +51,7 @@ process intersect_VCFs_BCFtools {
     }
 
  process plot_venn_R {
-     container params.docker_image_r_scripts
+     container params.docker_image_r_VennDiagram
      publishDir path: "${params.workflow_output_dir}/output",
          mode: "copy",
          pattern: "*.tiff"

From d003dd7c7c468adece389cc026a36d86d307c734 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Wed, 2 Aug 2023 12:02:11 -0700
Subject: [PATCH 15/16] plot_venn_R -> plot_VennDiagram_R

---
 module/intersect-processes.nf | 2 +-
 module/intersect.nf           | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index d5f5b700..6a8edf8a 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -50,7 +50,7 @@ process intersect_VCFs_BCFtools {
     """
     }
 
- process plot_venn_R {
+ process plot_VennDiagram_R {
      container params.docker_image_r_VennDiagram
      publishDir path: "${params.workflow_output_dir}/output",
          mode: "copy",
diff --git a/module/intersect.nf b/module/intersect.nf
index c6d0da24..cb4e2c7b 100644
--- a/module/intersect.nf
+++ b/module/intersect.nf
@@ -1,5 +1,5 @@
 include { generate_sha512sum } from './common'
-include { intersect_VCFs_BCFtools; plot_venn_R } from './intersect-processes.nf'
+include { intersect_VCFs_BCFtools; plot_VennDiagram_R } from './intersect-processes.nf'
 
 workflow intersect {
     // pass bin directory in project folder as channel into docker
@@ -24,7 +24,7 @@ workflow intersect {
                 .map{ it -> ["${file(it).getName().split('_')[0]}-SNV-idx", it]}
                 )
         generate_sha512sum(file_for_sha512)
-        plot_venn_R(
+        plot_VennDiagram_R(
             script_dir_ch,
             intersect_VCFs_BCFtools.out.isec_dir,
         )

From 33a591568d814de0d847dcff4977744ecb0da262 Mon Sep 17 00:00:00 2001
From: Sorel Fitz-Gibbon <sfitzgibbon@mednet.ucla.edu>
Date: Wed, 2 Aug 2023 14:56:25 -0700
Subject: [PATCH 16/16] rm BL-utils and move script_dir_ch definition

---
 config/F2.config              |  2 +-
 docker/plot-venn/Dockerfile   | 18 +++++++++---------
 main.nf                       | 16 +++++++++++++---
 module/intersect-processes.nf |  4 ++--
 module/intersect.nf           |  4 +---
 r-scripts/plot-venn.R         |  5 ++---
 6 files changed, 28 insertions(+), 21 deletions(-)

diff --git a/config/F2.config b/config/F2.config
index b7334aec..aaea5be5 100644
--- a/config/F2.config
+++ b/config/F2.config
@@ -1,4 +1,4 @@
-// Other processes after create_IndelCandidate_SAMtools will only run one at a time, so
+// Other processes will only run one at a time, so
 // we don't need to control their resources.
 // The configuration below forces processes to run one at a time by needing
 // the total memory available on a lowmem node.
diff --git a/docker/plot-venn/Dockerfile b/docker/plot-venn/Dockerfile
index ef47a4a3..12e5afcf 100644
--- a/docker/plot-venn/Dockerfile
+++ b/docker/plot-venn/Dockerfile
@@ -1,16 +1,16 @@
+ARG MINIFORGE_VERSION=22.9.0-2
 ARG UBUNTU_VERSION=20.04
-FROM ubuntu:${UBUNTU_VERSION}
 
-ARG DEBIAN_FRONTEND=noninteractive
+FROM condaforge/mambaforge:${MINIFORGE_VERSION} AS builder
 
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends libxml2 libxml2-dev libcurl4-gnutls-dev build-essential r-base r-base-dev \
-    libfontconfig1-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev r-cran-rgl \
-    git libssl-dev r-cran-curl && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
+RUN mamba create -qy -p /usr/local \
+        'r-base>=4.2.1' \
+        r-argparse \
+        r-VennDiagram
 
-RUN R -q -e 'install.packages(c("devtools", "argparse", "VennDiagram"))'
-RUN R -q -e 'devtools::install_github("uclahs-cds/public-R-BoutrosLab-utilities")'
+# Copy from builder into final image
+FROM ubuntu:${UBUNTU_VERSION} AS final
+COPY --from=builder /usr/local /usr/local
 
 # Add a new user/group called bldocker
 RUN groupadd -g 500001 bldocker \
diff --git a/main.nf b/main.nf
index 82745a97..d55b9b3b 100755
--- a/main.nf
+++ b/main.nf
@@ -84,8 +84,11 @@ include { muse } from './module/muse' addParams(
 
 include { intersect } from './module/intersect' addParams(
     workflow_output_dir: "${params.output_dir_base}/intersect-BCFtools-${params.BCFtools_version}",
-    workflow_log_output_dir: "${params.log_output_dir}/process-log/intersect-BCFtools-${params.BCFtools_version}"
-    )
+    workflow_log_output_dir: "${params.log_output_dir}/process-log/intersect-BCFtools-${params.BCFtools_version}",
+    output_filename: generate_standard_filename("Consensus",
+        params.dataset_id,
+        params.sample_id,
+        [:]))
 
 // Returns the index file for the given bam or vcf
 def indexFile(bam_or_vcf) {
@@ -117,12 +120,18 @@ Channel
         }
     .set { normal_input }
 
+    script_dir_ch = Channel.fromPath(
+        "$projectDir/r-scripts",
+        checkIfExists: true
+        )
+
 workflow {
     reference_ch = Channel.from(
         params.reference,
         params.reference_index,
         params.reference_dict
         )
+
     // Input file validation
     if (params.tumor_only_mode) {
         file_to_validate = reference_ch
@@ -227,7 +236,8 @@ workflow {
 
         intersect(
             tool_vcfs,
-            tool_indices
+            tool_indices,
+            script_dir_ch
             )
         }
     }
diff --git a/module/intersect-processes.nf b/module/intersect-processes.nf
index 6a8edf8a..91e50374 100644
--- a/module/intersect-processes.nf
+++ b/module/intersect-processes.nf
@@ -4,7 +4,7 @@ log.info """\
 ====================================
 Docker Images:
 - docker_image_BCFtools: ${params.docker_image_BCFtools}
-- docker_image_r_scripts: ${params.docker_image_r_VennDiagram}
+- docker_image_r_VennDiagram: ${params.docker_image_r_VennDiagram}
 ====================================
 """
 process intersect_VCFs_BCFtools {
@@ -71,6 +71,6 @@ process intersect_VCFs_BCFtools {
      script:
      """
      set -euo pipefail
-     Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --dataset ${params.dataset_id}
+     Rscript ${script_dir}/plot-venn.R --isec_dir ${isec_dir} --outfile ${params.output_filename}_Venn-diagram.tiff
      """
      }
diff --git a/module/intersect.nf b/module/intersect.nf
index cb4e2c7b..c0084dec 100644
--- a/module/intersect.nf
+++ b/module/intersect.nf
@@ -2,12 +2,10 @@ include { generate_sha512sum } from './common'
 include { intersect_VCFs_BCFtools; plot_VennDiagram_R } from './intersect-processes.nf'
 
 workflow intersect {
-    // pass bin directory in project folder as channel into docker
-    script_dir_ch = Channel.fromPath("$projectDir/r-scripts", checkIfExists: true)
-
     take:
     tool_vcfs
     tool_indices
+    script_dir_ch
 
     main:
         intersect_VCFs_BCFtools(
diff --git a/r-scripts/plot-venn.R b/r-scripts/plot-venn.R
index c51ff605..501264e7 100644
--- a/r-scripts/plot-venn.R
+++ b/r-scripts/plot-venn.R
@@ -8,13 +8,12 @@
 
 ## Setup the environment ###########################################################################
 library('argparse');
-library('BoutrosLab.utilities');
 library('VennDiagram');
 
 ## Parse the arguments #############################################################################
 parser <- ArgumentParser();
 parser$add_argument('-i', '--isec_dir', help = 'The directory containing the output from BCFtools intersect', type = 'character');
-parser$add_argument('-d', '--dataset', help = 'The dataset ID passed from nextflow', type = 'character');
+parser$add_argument('-o', '--outfile', help = 'Output filename', type = 'character');
 args <- parser$parse_args();
 
 ## Function: plot venn diagram #####################################################################
@@ -48,4 +47,4 @@ colnames(sites) <- header
 variants <- paste(sites$chrom, sites$pos, sep = '_');
 tool.variants <- lapply(sites[, algorithms], function(x) variants[x == 1])
 tool.variants.ordered <- tool.variants[order(lengths(tool.variants), decreasing = TRUE)];
-plot.venn(tool.variants.ordered, generate.filename(args$dataset, 'Venn-diagram', 'tiff'));
+plot.venn(tool.variants.ordered, args$outfile);