Merge branch 'dev' into nf-core-template-merge-3.2.0

.editorconfig

@@ -35,3 +35,13 @@ indent_style = unset
 # ignore ro-crate metadata files
 [**/ro-crate-metadata.json]
 insert_final_newline = unset
+
+# ignore embedded libraries and third-party code
+[assets/main_report/_extensions/**]
+charset = unset
+end_of_line = unset
+insert_final_newline = unset
+trim_trailing_whitespace = unset
+indent_style = unset
+indent_size = unset
+

.gitignore

@@ -7,3 +7,16 @@ testing/
 testing*
 *.pyc
 null/
+scratch/
+*.swp
+.Rproj.user
+*.Rproj
+.Rhistory
+assets/*.html
+README.html
+.~*
+seqtk_sample/
+docs/lab_meetings
+path_surveil_data
+.RData
+

.nf-core.yml

@@ -4,12 +4,12 @@ lint:
 nf_core_version: 3.2.0
 repository_type: pipeline
 template:
-  author: "Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I.\
-    \ Bocardo, Hung Phan, Je\uFB00 H. Chang, Niklaus J. Gr\xFCnwald"
+  author: "Zachary S.L. Foster, Martha Sudermann, Nicholas C. Cauldron, Fernanda I.
+    Bocardo, Hung Phan, Jeff H. Chang, Niklaus J. Grünwald"
   description: Surveillance of plant pathogens using high-throughput sequencing
   force: false
   is_nfcore: true
   name: pathogensurveillance
   org: nf-core
   outdir: .
-  version: 1.0dev
+  version: 1.0.0

.prettierignore

@@ -11,3 +11,4 @@ testing*
 *.pyc
 bin/
 ro-crate-metadata.json
+assets/main_report

assets/.gitignore

@@ -0,0 +1,2 @@
+bakta_db
+

assets/main_report/.gitignore

@@ -0,0 +1,9 @@
+/.quarto/
+_book
+_site
+*_files
+*.html
+*.ipynb
+_test_data/**/quast
+_test_data/**/multiqc
+packages.bib

assets/main_report/README.md

@@ -0,0 +1,6 @@
+# Citations
+
+Add new citations to:
+
+1. assets/main_report/citations.bib (full .bib citation)
+2. assets/main_report/citations.csv (column 1: process name; column 2: @bib in-text citation)

assets/main_report/_extensions/mcanouil/iconify/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Mickaël Canouil
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

assets/main_report/_extensions/mcanouil/iconify/_extension.yml

@@ -0,0 +1,7 @@
+title: Iconify support
+author: Mickaël Canouil
+version: 2.1.2
+quarto-required: ">=1.2.280"
+contributes:
+  shortcodes:
+    - iconify.lua

assets/main_report/_extensions/mcanouil/iconify/iconify.lua

@@ -0,0 +1,156 @@
+--[[
+# MIT License
+#
+# Copyright (c) Mickaël Canouil
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+]]
+
+local function ensure_html_deps()
+  quarto.doc.add_html_dependency({
+    name = 'iconify',
+    version = '2.1.0',
+    scripts = {"iconify-icon.min.js"}
+  })
+end
+
+local function is_empty(s)
+  return s == nil or s == ''
+end
+
+local function is_valid_size(size)
+  if is_empty(size) then
+    return ''
+  end
+  local size_table = {
+    ["tiny"]         = "0.5em",
+    ["scriptsize"]   = "0.7em",
+    ["footnotesize"] = "0.8em",
+    ["small"]        = "0.9em",
+    ["normalsize"]   = "1em",
+    ["large"]        = "1.2em",
+    ["Large"]        = "1.5em",
+    ["LARGE"]        = "1.75em",
+    ["huge"]         = "2em",
+    ["Huge"]         = "2.5em",
+    ["1x"]           = "1em",
+    ["2x"]           = "2em",
+    ["3x"]           = "3em",
+    ["4x"]           = "4em",
+    ["5x"]           = "5em",
+    ["6x"]           = "6em",
+    ["7x"]           = "7em",
+    ["8x"]           = "8em",
+    ["9x"]           = "9em",
+    ["10x"]          = "10em",
+    ["2xs"]          = "0.625em",
+    ["xs"]           = "0.75em",
+    ["sm"]           = "0.875em",
+    ["lg"]           = "1.25em",
+    ["xl"]           = "1.5em",
+    ["2xl"]          = "2em"
+  }
+  for key, value in pairs(size_table) do
+    if key == size then
+      return 'font-size: ' .. value .. ';'
+    end
+  end
+  return 'font-size: ' .. size .. ';'
+end
+
+return {
+  ["iconify"] = function(args, kwargs)
+    -- detect html (excluding epub which won't handle fa)
+    if quarto.doc.is_format("html:js") then
+      ensure_html_deps()
+      local icon = pandoc.utils.stringify(args[1])
+      local set = "fluent-emoji"
+
+      if #args > 1 and string.find(pandoc.utils.stringify(args[2]), ":") then
+        quarto.log.warning(
+          'Use "set:icon" or "set icon" syntax, not both! ' ..
+          'Using "set:icon" syntax and discarding first argument!'
+        )
+        icon = pandoc.utils.stringify(args[2])
+      end
+
+      if string.find(icon, ":") then
+        set = string.sub(icon, 1, string.find(icon, ":") - 1)
+        icon = string.sub(icon, string.find(icon, ":") + 1)
+      elseif #args > 1 then
+        set = icon
+        icon = pandoc.utils.stringify(args[2])
+      end
+
+      local attributes = ' icon="' .. set .. ':' .. icon .. '"'
+      local default_label = 'Icon ' .. icon .. ' from ' .. set .. ' Iconify.design set.'
+
+      local size = is_valid_size(pandoc.utils.stringify(kwargs["size"]))
+      if not is_empty(size) then
+        attributes = attributes .. ' style="' .. size .. '"'
+      end
+
+      local aria_label = pandoc.utils.stringify(kwargs["label"])
+      if is_empty(aria_label) then
+        aria_label =  ' aria-label="' .. default_label .. '"'
+      else
+        aria_label =  ' aria-label="' .. aria_label .. '"'
+      end
+
+      local title = pandoc.utils.stringify(kwargs["title"])
+      if is_empty(title) then
+        title =  ' title="' .. default_label .. '"'
+      else
+        title =  ' title="' .. title .. '"'
+      end
+
+      attributes = attributes .. aria_label .. title
+
+      local width = pandoc.utils.stringify(kwargs["width"])
+      if not is_empty(width) and is_empty(size) then
+        attributes = attributes .. ' width="' .. width .. '"'
+      end
+      local height = pandoc.utils.stringify(kwargs["height"])
+      if not is_empty(height) and is_empty(size)  then
+        attributes = attributes .. ' height="' .. height .. '"'
+      end
+      local flip = pandoc.utils.stringify(kwargs["flip"])
+      if not is_empty(flip) then
+        attributes = attributes .. ' flip="' .. flip.. '"'
+      end
+      local rotate = pandoc.utils.stringify(kwargs["rotate"])
+      if not is_empty(rotate) then
+        attributes = attributes .. ' rotate="' .. rotate .. '"'
+      end
+
+      local inline = pandoc.utils.stringify(kwargs["inline"])
+      if is_empty(inline) or inline ~= "false" then
+        attributes = ' inline ' .. attributes
+      end
+
+
+      return pandoc.RawInline(
+        'html',
+        '<iconify-icon role="img"' .. attributes .. '></iconify-icon>'
+      )
+    else
+      return pandoc.Null()
+    end
+  end
+}

assets/main_report/_extensions/quarto-ext/fontawesome/_extension.yml

@@ -0,0 +1,7 @@
+title: Font Awesome support
+author: Carlos Scheidegger
+version: 1.1.0
+quarto-required: ">=1.2.269"
+contributes:
+  shortcodes:
+    - fontawesome.lua