From a6f3c680d3a9991da9983d98dd4d76211f4bdfcd Mon Sep 17 00:00:00 2001
From: "Zachary S.L. Foster" <zacharyfoster1989@gmail.com>
Date: Fri, 19 Jan 2024 15:55:16 -0800
Subject: [PATCH] add ggdendro to dockerfile

---
 assets/main_report/index.qmd                  | 14 +-------------
 dockerfiles/main-report-r-packages/Dockerfile |  1 +
 modules/local/main_report.nf                  |  2 +-
 3 files changed, 3 insertions(+), 14 deletions(-)

diff --git a/assets/main_report/index.qmd b/assets/main_report/index.qmd
index 1e6305f7..836bceb7 100644
--- a/assets/main_report/index.qmd
+++ b/assets/main_report/index.qmd
@@ -38,6 +38,7 @@ library(plotly)
 library(webshot2)
 library(metacoder)
 library(psminer)
+library(ggdendro)
 ```
 
 ```{r parse_inputs}
@@ -112,10 +113,6 @@ Perhaps a table with a list of majors steps and a icon next to each for done/que
 ## Sample plotly/ggtree tree from [here](https://plotly.com/ggplot2/dendrogram/)
 
 ```{r}
-library(plotly)
-library(ggplot2)
-library(ggdendro)
-
 model <- hclust(dist(USArrests), "ave")
 dhc <- as.dendrogram(model)
 
@@ -133,15 +130,6 @@ ggplotly(p)
 ## {{< bi clipboard-data >}} Input data
 
 ```{r}
-# samp_data %>%
-#     select(
-#         `Sample ID`=sample,
-#         `Forward Reads`=fastq_1,
-#         `Reverse Reads`=fastq_2,
-#         `Reference ID`=reference_id,
-#         `Reference`=reference) %>%
-#     DT::datatable()
-
 print_sample_metadata(samp_data, interactive = knitr::is_html_output())
 ```
 
diff --git a/dockerfiles/main-report-r-packages/Dockerfile b/dockerfiles/main-report-r-packages/Dockerfile
index 3a16f5dc..fcd1da9e 100644
--- a/dockerfiles/main-report-r-packages/Dockerfile
+++ b/dockerfiles/main-report-r-packages/Dockerfile
@@ -58,6 +58,7 @@ install.r \
     plotly \
     webshot2 \
     metacoder \
+    ggdendro
 EOF
 
 RUN <<EOF
diff --git a/modules/local/main_report.nf b/modules/local/main_report.nf
index 84a8645d..f6cb950e 100644
--- a/modules/local/main_report.nf
+++ b/modules/local/main_report.nf
@@ -5,7 +5,7 @@ process MAIN_REPORT {
     conda "conda-forge::quarto conda-forge::r-knitr" // TODO: it just uses the local computers R packages for now
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/main-report-r-packages':
-        'docker.io/zacharyfoster/main-report-r-packages:0.3' }"
+        'docker.io/zacharyfoster/main-report-r-packages:0.4' }"
 
     input:
     tuple val(group_meta), val(ref_metas), file(sendsketchs), file(quast_dirs), file(vcfs), file(snp_aligns), file(snp_phylos), file(ani_matrix), file(core_phylo)