feat: add datavzrd wrapper (#535)

* initial datavzrd wrapper * Update utils/datavzrd/meta.yaml Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com> * Update Snakefile * Update meta.yaml * Update meta.yaml * Update utils/datavzrd/test/Snakefile Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> * Update utils/datavzrd/test/Snakefile Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> * Update utils/datavzrd/meta.yaml Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> * Update utils/datavzrd/environment.yaml Co-authored-by: Johannes Köster <johannes.koester@uni-due.de> Co-authored-by: Filipe G. Vieira <fgarrettvieira@gmail.com> Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
snakemake · Aug 18, 2022 · 8c05064 · 8c05064
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diff --git a/utils/datavzrd/environment.yaml b/utils/datavzrd/environment.yaml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - datavzrd =1.17
diff --git a/utils/datavzrd/meta.yaml b/utils/datavzrd/meta.yaml
@@ -0,0 +1,10 @@
+name: datavzrd
+description: |
+  datavzrd allows to render tables by providing a configuration file. 
+  Configuration templates can be dynamically customized by utilizing the 
+  `rendering integration <https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#template-rendering-integration>`_.
+  Any files specified in the configuration file have to be also specified as additional input files in the
+  datavzrd rule.
+url: https://github.com/koesterlab/datavzrd
+authors:
+  - Felix Mölder
diff --git a/utils/datavzrd/test/Snakefile b/utils/datavzrd/test/Snakefile
@@ -0,0 +1,21 @@
+rule all:  # [hide]
+    input:  # [hide]
+        "results/datavzrd-report/A",  # [hide]
+
+
+rule datavzrd:
+    input:
+        config="resources/{sample}.datavzrd.yaml",
+        # optional files required for rendering the given config
+        table="data/A.tsv",
+    output:
+        report(
+            directory("results/datavzrd-report/{sample}"),
+            htmlindex="index.html",
+            # see https://snakemake.readthedocs.io/en/stable/snakefiles/reporting.html
+            # for additional options like caption, categories and labels
+        ),
+    log:
+        "logs/datavzrd_report/{sample}.log",
+    wrapper:
+        "master/utils/datavzrd"
diff --git a/utils/datavzrd/test/data/A.tsv b/utils/datavzrd/test/data/A.tsv
@@ -0,0 +1,3 @@
+symbol	gene	feature	impact	hgvsp
+PTEN	ENSG00000171862	ENST00000371953	HIGH	ENSP00000361021.3:p.Arg335Ter
+FGFR	ENSG00000145675	ENST00000521381	HIGH	ENSP00000428056.1:p.Tyr580Ter
diff --git a/utils/datavzrd/test/resources/A.datavzrd.yaml b/utils/datavzrd/test/resources/A.datavzrd.yaml
@@ -0,0 +1,12 @@
+name: My variant report
+datasets:
+  variants:
+    path: "data/A.tsv"
+    separator: "\t"
+
+default-view: variants
+views:
+  variants:
+    dataset: variants
+    desc: |
+      ### Some crazy variants
diff --git a/utils/datavzrd/wrapper.py b/utils/datavzrd/wrapper.py
@@ -0,0 +1,10 @@
+__author__ = "Johannes Köster"
+__copyright__ = "Copyright 2017, Johannes Köster"
+__email__ = "johannes.koester@protonmail.com"
+__license__ = "MIT"
+
+from snakemake.shell import shell
+
+log = snakemake.log_fmt_shell(stdout=True, stderr=True)
+
+shell("datavzrd {snakemake.input.config} --output {snakemake.output[0]} {log}")