update README to change name to PathogenDx

README.md

@@ -1,33 +1,34 @@
-# ![nf-core/plantpathsurveil](docs/images/nf-core-plantpathsurveil_logo_light.png#gh-light-mode-only) ![nf-core/plantpathsurveil](docs/images/nf-core-plantpathsurveil_logo_dark.png#gh-dark-mode-only)
+# ![nf-core/pathogendx](docs/images/nf-core-pathogendx_logo_light.png#gh-light-mode-only) ![nf-core/pathogendx](docs/images/nf-core-pathogendx_logo_dark.png#gh-dark-mode-only)
 
-[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/plantpathsurveil/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
+[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pathogendx/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
 
 [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
 [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
 [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
 [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)
-[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/plantpathsurveil)
+[![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/pathogendx)
 
-[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23plantpathsurveil-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/plantpathsurveil)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23pathogendx-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/pathogendx)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core)
+
+## NOTE: THIS PROJECT IS UNDER DEVLOPMENT AND MAY NOT FUNCTION AS EXPECTED UNTIL THIS MESSAGE GOES AWAY
 
 ## Introduction
 
 <!-- TODO nf-core: Write a 1-2 sentence summary of what data the pipeline is for and what it does -->
 
-**nf-core/plantpathsurveil** is a population genomic pipeline for pathogen diagnosis, variant detection, and biosurveillance.
+**nf-core/pathogendx** is a population genomic pipeline for pathogen diagnosis, variant detection, and biosurveillance.
+The pipeline accepts the paths to raw reads for one or more organisms and creates reports in the form of HTML websites or PDF documents.
+Significant features include the ability to analyze unidentified eukaryotic and prokaryotic samples, creation of reports for multiple user-defined groupings of samples, automated discovery and downloading of reference assemblies from NCBI RefSeq, and rapid initial identification based on k-mer sketches followed by a more robust core genome phylogeny.
 
 The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community!
 
 <!-- TODO nf-core: Add full-sized test dataset and amend the paragraph below if applicable -->
 
-On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/plantpathsurveil/results).
+On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world data sets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources.The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/pathogendx/results).
 
 ## Pipeline summary
 
-<!-- TODO nf-core: Fill in short bullet-pointed list of the default steps in the pipeline -->
-
-1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
-2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
+![Pipeline flowchart](docs/posters/pipeline_diagram.png)
 
 ## Quick Start
 
@@ -38,7 +39,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
 3. Download the pipeline and test it on a minimal dataset with a single command:
 
    ```bash
-   nextflow run nf-core/plantpathsurveil -profile test,YOURPROFILE --outdir <OUTDIR>
+   nextflow run nf-core/pathogendx -profile test,YOURPROFILE --outdir <OUTDIR>
    ```
 
    Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string.
@@ -53,16 +54,16 @@ On release, automated continuous integration tests run the pipeline on a full-si
    <!-- TODO nf-core: Update the example "typical command" below used to run the pipeline -->
 
    ```bash
-   nextflow run nf-core/plantpathsurveil --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
+   nextflow run nf-core/pathogendx --input samplesheet.csv --outdir <OUTDIR> --genome GRCh37 -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
    ```
 
 ## Documentation
 
-The nf-core/plantpathsurveil pipeline comes with documentation about the pipeline [usage](https://nf-co.re/plantpathsurveil/usage), [parameters](https://nf-co.re/plantpathsurveil/parameters) and [output](https://nf-co.re/plantpathsurveil/output).
+The nf-core/pathogendx pipeline comes with documentation about the pipeline [usage](https://nf-co.re/pathogendx/usage), [parameters](https://nf-co.re/pathogendx/parameters) and [output](https://nf-co.re/pathogendx/output).
 
 ## Credits
 
-nf-core/plantpathsurveil was originally written by Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald.
+nf-core/pathogendx was originally written by Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I. Bocardo, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald.
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
@@ -72,12 +73,12 @@ We thank the following people for their extensive assistance in the development
 
 If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
 
-For further information or help, don't hesitate to get in touch on the [Slack `#plantpathsurveil` channel](https://nfcore.slack.com/channels/plantpathsurveil) (you can join with [this invite](https://nf-co.re/join/slack)).
+For further information or help, don't hesitate to get in touch on the [Slack `#pathogendx` channel](https://nfcore.slack.com/channels/pathogendx) (you can join with [this invite](https://nf-co.re/join/slack)).
 
 ## Citations
 
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
-<!-- If you use  nf-core/plantpathsurveil for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
+<!-- If you use  nf-core/pathogendx for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
 <!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
 

assets/main_report/01-identification.Rmd

@@ -13,16 +13,17 @@ params = lapply(params, function(x) file.path(work_dir, x))
 ```
 
 
-```{r setup, include=FALSE}
+```{r id_setup, include=FALSE}
 knitr::opts_chunk$set(echo = FALSE, fig.width = 10, warning = FALSE)
 ```
 
-```{r libraries}
+```{r id_libraries}
 library(phylocanvas)
 library(ape)
+library(magrittr)
 ```
 
-```{r parse_inputs}
+```{r id_parse_inputs}
 ref_meta <- read.csv(params$ref_data, sep = '\t')
 ref_meta$modified_id <- gsub(ref_meta$LastMajorReleaseAccession, pattern = ".", replacement = "_", fixed = TRUE)
 samp_meta <- read.csv(params$samp_data, sep = ',')
@@ -33,10 +34,13 @@ snp_trees <- ape::read.tree(params$snp_phylos)
 ```
 
 
+## Initial ANI tree
+
+
 ## Core genome phylogeny
 
 
-```{r core_phylo, fig.height = 7, eval = ! is.null(core_tree)}
+```{r id_core_phylo, fig.height = 7, eval = ! is.null(core_tree)}
 # Identify which tips are samples and references
 sample_ids <- core_tree$tip.label[core_tree$tip.label %in% samp_meta$modified_id]
 
@@ -60,29 +64,19 @@ core_tree$tip.label <- name_key[core_tree$tip.label]
 
 # Plot tree
 phycanv <- phylocanvas(core_tree, treetype = "rectangular", alignlabels = T, showscalebar = T, width = "100%")
+for (x in name_key[sample_ids]) {
+  phycanv <- style_node(phycanv, x, labelcolor = "green", labeltextsize = 30)
+}
+    
 phycanv
 ```
 
-```{asis no_core_phylo, echo = is.null(core_tree)}
+```{asis id_no_core_phylo, echo = is.null(core_tree)}
 There is no tree to draw, probably because there were too few samples.
 More info will be added later.
 ```
 
 
 
-## SNP phylogeny
-
 
-```{r snp_phylo, fig.height = 7, eval = ! is.null(snp_trees)}
-# Root tree 
-snp_trees <- root(snp_trees, "REF")
 
-# Plot tree
-phycanv <- phylocanvas(snp_trees, treetype = "rectangular", alignlabels = T, showscalebar = T, width = "100%")
-phycanv
-```
-
-```{asis no_snp_phylo, echo = is.null(snp_trees)}
-There is no tree to draw, probably because there were too few samples.
-More info will be added later.
-```

assets/main_report/_output.yml

@@ -3,11 +3,21 @@ bookdown::gitbook:
   config:
     toc:
       before: |
-        <li><a href="./">PathogenDx Report</a></li>
+        <li><b><a href="./">PathogenDx Report</a></b></li>
       after: |
         <li><a href="https://github.com/rstudio/bookdown" target="blank">Created with bookdown</a></li>
-    edit: https://github.com/USERNAME/REPO/edit/BRANCH/%s
+    # edit: null
     download: ["pdf", "epub"]
+    sharing:
+      facebook: false
+      github: true
+      twitter: false
+      linkedin: false
+      weibo: false
+      instapaper: false
+      vk: false
+      whatsapp: false
+      all: false
 bookdown::pdf_book:
   includes:
     in_header: preamble.tex

assets/main_report/index.Rmd

@@ -23,6 +23,10 @@ params:
 This is the first page a user sees.
 What should go here?
 
+## Input settings
+
+## Software used
+
 
 ```{r include=FALSE}
 # automatically create a bib database for R packages

bin/sendsketch_filter.R

@@ -1,4 +1,4 @@
-#!/usr/bin/env -S Rscript --vanilla
+#!/usr/bin/env Rscript
 
 # Options
 ani_threshold <- c(species = 90, genus = 90, family = 70)  # These numbers are total guesses. TODO: find reasonable defaults (issue #11)
@@ -34,3 +34,4 @@ writeLines(kingdom, "kingdom.txt")
 
 # Save full taxonomic classification
 writeLines(data$taxonomy[1], "classification.txt")
+