-
Notifications
You must be signed in to change notification settings - Fork 185
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* 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>
- Loading branch information
1 parent
8c4d1cb
commit 8c05064
Showing
6 changed files
with
61 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,5 @@ | ||
channels: | ||
- conda-forge | ||
- nodefaults | ||
dependencies: | ||
- datavzrd =1.17 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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}") |