feat: General report chls

.github/workflows/release-please.yaml

@@ -16,3 +16,4 @@ jobs:
           default-branch: main
           extra-files:
             - workflow/templates/cnv_html_report/index.html
+            - workflow/templates/general_html_report/index.html

.gitignore

@@ -7,3 +7,5 @@ reports/
 site/
 logs/
 results/
+tailwindcss
+*.min.css

.prettierignore

@@ -0,0 +1 @@
+workflow/templates/assets/css/main.css

.tests/integration/Snakefile_module

@@ -4,6 +4,7 @@ from hydra_genetics.utils.misc import get_module_snakefile
 rule all:
     input:
         "reports/cnv_html_report/NA12878_N.pathology.cnv_report.html",
+        "reports/general_html_report/NA12878_N.general_report.html",
 
 
 module reports:

.tests/integration/config.yaml

@@ -1,4 +1,5 @@
 output: "../../config/output_files.yaml"
+general_report: "../../config/general_report.yaml"
 resources: "resources.yaml"
 samples: "samples.tsv"
 units: "units.tsv"
@@ -9,6 +10,10 @@ reference:
 cnv_html_report:
   cytobands: true
 
+general_html_report:
+  final_directory_depth: 2
+
+
 merge_cnv_json:
   annotations:
     - config/amp_genes.bed

.tests/integration/config/NA12878_N.general_report.json

@@ -0,0 +1,62 @@
+{
+  "sample": "NA12878",
+  "analysis_date": "2023-11-17",
+  "pipeline": {
+    "name": "Twist Solid",
+    "version": "0.9.0",
+    "uri": "https://github.com/genomic-medicine-sweden/Twist_Solid/tree/v0.9.0"
+  },
+  "file_links": [
+    {
+      "name": "CNV HTML report",
+      "description": "HTML report summarising the results of the CNV analysis",
+      "uri": "results/cnv/NA12878_N.pathology.cnv_report.html"
+    }
+  ],
+  "results": [
+    {
+      "name": "TMB",
+      "type": "single_value",
+      "description": "Tumor mutational burden",
+      "value": 12
+    },
+    {
+      "name": "Result 2",
+      "type": "table",
+      "description": "A table of results",
+      "value": [
+        {
+          "column1": "row1",
+          "column2": "value1"
+        },
+        {
+          "column1": "row2",
+          "column2": "value2"
+        },
+        {
+          "column2": "value3",
+          "column1": "row3"
+        }
+      ]
+    },
+    {
+      "name": "Image result",
+      "type": "image",
+      "description": "An image",
+      "value": "https://placehold.co/600x400/png"
+    },
+    {
+      "name": "Local image",
+      "type": "image",
+      "description": "A local image from a path relative to the analysis directory",
+      "value": "test_data/NA12878_N.png"
+    },
+    {
+      "name": "QC",
+      "type": "multiqc",
+      "description": "QC data from MultiQC with the other samples in the sampe run included for context",
+      "sections": ["table"],
+      "value": "qc/multiqc/multiqc_DNA_data/multiqc_data.json"
+    }
+  ]
+}

.tests/unit/test_general_html_report.py

@@ -0,0 +1,81 @@
+import pathlib
+import pytest
+import sys
+
+sys.path.insert(0, str(pathlib.Path(__file__).parents[2]))
+
+from workflow.scripts.general_html_report import *
+
+
+def test_valid_table():
+    table = [
+        {
+            "col1": "val1",
+            "col2": 1,
+        },
+        {
+            "col1": "val2",
+            "col2": 2,
+        },
+        {
+            "col1": "val3",
+            "col2": 3,
+        },
+    ]
+
+    assert validate_table_data(table)
+
+
+def test_empty_table():
+    with pytest.raises(ValueError, match="empty table"):
+        validate_table_data([])
+
+
+def test_unequal_columns():
+    table = [
+        {
+            "col1": "val1",
+            "col2": 1,
+        },
+        {
+            "col1": "val2",
+            "col3": 2,
+        },
+        {
+            "col1": "val3",
+            "col2": 3,
+        },
+    ]
+
+    with pytest.raises(
+        ValueError,
+        match="expected columns 'col1', 'col2' in row 2, found 'col1', 'col3'",
+    ):
+        validate_table_data(table)
+
+
+def test_missing_columns():
+    table = [
+        {
+            "col1": "val1",
+            "col2": 1,
+        },
+        {
+            "col1": "val2",
+        },
+        {
+            "col1": "val3",
+            "col2": 3,
+        },
+    ]
+
+    with pytest.raises(ValueError, match="expected 2 columns in row 2, found 1"):
+        validate_table_data(table)
+
+
+def test_fix_relative_uri():
+    assert fix_relative_uri("http://www.google.com", depth=2) == "http://www.google.com"
+    assert fix_relative_uri("https://www.google.com", depth=2) == "https://www.google.com"
+    assert fix_relative_uri("docker://hydra-genetics/picard", depth=2) == "docker://hydra-genetics/picard"
+    assert fix_relative_uri("/path/to/a/file.txt", depth=2) == "/path/to/a/file.txt"
+    assert fix_relative_uri("path/to/a/file.txt", depth=2) == "../../path/to/a/file.txt"

config/config.yaml

@@ -1,5 +1,6 @@
 ---
 output: "config/output_files.yaml"
+general_report: "config/general_report.yaml"
 resources: "config/resources.yaml"
 samples: "samples.tsv"
 units: "units.tsv"
@@ -14,6 +15,9 @@ cnv_html_report:
   cytobands: false
   show_table: true
 
+general_html_report:
+  final_directory_depth: 2
+
 merge_cnv_json:
   annotations:
   cytobands:

config/general_report.yaml

@@ -0,0 +1,6 @@
+files:
+  - name: CNV report 
+    type: file_link
+    description: Link to CNV HTML report
+    input: results/dna/cnv/{sample}_{type}/{sample}_{type}.pathology_purecn.cnv.html
+    nav_header: CNV

config/output_files.yaml

@@ -2,3 +2,10 @@ files:
   - name: "CNV HTML report"
     input: "reports/cnv_html_report/{sample}_{type}.pathology.cnv_report.html"
     output: "results/cnv/{sample}_{type}.pathology.cnv_report.html"
+    types:
+      - T
+  - name: "General Report"
+    input: "reports/general_html_report/{sample}_{type}.general_report.html"
+    output: "results/dna/reports/{sample}_{type}.general_report.html"
+    types:
+      - T

docs/softwares.md

@@ -65,3 +65,25 @@ Merge JSON files from multiple CNV callers and add annotations and other sample
 #### Resources settings (`resources.yaml`)
 
 #RESOURCESSCHEMA__merge_cnv_json#
+
+## general_html_report
+
+Generate a general HTML report for a single sample.
+
+### :snake: Rule
+
+#SNAKEMAKE_RULE_SOURCE__general_html_report__general_html_report#
+
+#### :left_right_arrow: input / output files
+
+#SNAKEMAKE_RULE_TABLE__general_html_report__general_html_report#
+
+### :wrench: Configuration
+
+#### Software settings (`config.yaml`)
+
+#CONFIGSCHEMA__general_html_report#
+
+#### Resources settings (`resources.yaml`)
+
+#RESOURCESSCHEMA__general_html_report#

docs/tailwind.md

@@ -0,0 +1,30 @@
+# Tailwind CSS
+
+All reports in this repository share a single CSS file by default, and the content of this file is managed by [Tailwind](https://tailwindcss.com). This is a CSS framework that works with a very large number of minimal classes, which makes the styling very flexible without you having to write a single line of CSS. Since only the classes that are actually being used are included, the size of the resulting file can be kept down.
+
+## Setup
+
+Tailwind is available through [npm](https://www.npmjs.com/package/tailwindcss), but since there are no other Node.js dependencies in this project, it is recommended that you install the [standalone CLI tool](https://tailwindcss.com/blog/standalone-cli) instead. The binaries for various systems are [hosted on Github](https://github.com/tailwindlabs/tailwindcss/releases). Here is how to install on Linux:
+
+```bash
+curl -sLO https://github.com/tailwindlabs/tailwindcss/releases/download/v3.3.6/tailwindcss-linux-x64
+chmod +x tailwindcss-linux-x64
+mv tailwindcss-linux-x64 tailwindcss
+```
+
+Preferrably move this binary to a directory in your `$PATH`. Depending on the platform, the installation procedure might look different.
+
+## Usage
+
+The Tailwind configuration can be found in `tailwind.config.js`. By default, it will look for classes in all HTML and JS files in the `workflow/templates` directory. When actively working on a template, it is recommended that Tailwind is set to watch files for changes and edit the CSS file as it goes:
+
+```bash
+tailwindcss \
+    -i ./workflow/templates/assets/css/tailwind.css \
+    -o ./workflow/templates/assets/css/main.css \
+    --watch
+```
+
+In the example above, `./workflow/templates/assets/css/tailwind.css` is the input css file, and `./workflow/templates/assets/css/main.css` is the output css file which is used in the each template. This approach will make certain that each and every Tailwind class in use is available in the generated CSS file, and at the same time remove any unused classes.
+
+When including this file in a template, it is recommended that it is minified. In order to keep the git history clean, the minified CSS should not be committed to the repo, but rather be something that is generated by the script of each individual report. <!-- TODO: add a reference to an example, as soon as there is one -->

mkdocs.yaml

@@ -3,6 +3,8 @@ nav:
   - Introduction: intro.md
   - Reports: reports.md
   - Softwares: softwares.md
+  - Development:
+      - Tailwind CSS: tailwind.md
 
 theme: readthedocs
 extra_css: [extra.css]

tailwind.config.js

@@ -0,0 +1,8 @@
+/** @type {import('tailwindcss').Config} */
+module.exports = {
+  content: ["workflow/templates/**/*.{html,js}"],
+  theme: {
+    extend: {},
+  },
+  plugins: [],
+};

workflow/Snakefile

@@ -6,6 +6,7 @@ __license__ = "GPL-3"
 
 # Include pipeline specific rules
 include: "rules/common.smk"
+include: "rules/general_html_report.smk"
 include: "rules/cnv_html_report.smk"
 
 

workflow/rules/common.smk

@@ -13,7 +13,7 @@ import yaml
 from snakemake.io import Wildcards
 from snakemake.utils import validate
 from snakemake.utils import min_version
-
+from datetime import datetime
 from hydra_genetics.utils.resources import load_resources
 from hydra_genetics.utils.samples import *
 from hydra_genetics.utils.units import *
@@ -45,6 +45,7 @@ units = (
 
 validate(units, schema="../schemas/units.schema.yaml")
 
+
 with open(config["output"]) as output:
     if config["output"].endswith("json"):
         output_spec = json.load(output)
@@ -53,6 +54,12 @@ with open(config["output"]) as output:
 
 validate(output_spec, schema="../schemas/output_files.schema.yaml")
 
+with open(config["general_report"]) as f:
+    if f.name.endswith(".yaml"):
+        general_report = yaml.safe_load(f)
+
+validate(general_report, "../schemas/general_report.schema.yaml")
+
 
 ### Set wildcard constraints
 wildcard_constraints: