rm BL-utils and move script_dir_ch definition

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.

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 \

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
             )
         }
     }

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
      """
      }

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(

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);