WIP: create reports with python

.gitignore

@@ -9,6 +9,7 @@ samples.yaml
 *.png
 *.rds
 *.html
+!spacemake/report/templates/*.html
 *.csv
 *.pdf
 *.txt.gz

environment.yaml

@@ -14,14 +14,7 @@ dependencies:
     - bcl2fastq2>=2.19
     - fastqc>=0.11.9
     - pip>=21.1
-    - r-base>=4.0.3
-    - r-rmarkdown>=2.7
-    - r-tidyverse>=1.3.1
-    - r-kableextra>=1.3.4
-    - r-cowplot>=1.1.1
-    - r-pals>=1.7
-    - r-hexbin
-    - r-scales
+    - jinja2>=3.1.2
     - pysam>=0.16.0.1
     - pot
     - openjdk==11.0.15

setup.cfg

@@ -32,6 +32,7 @@ spacemake =
     data/*.csv
     config/*.yaml
     longread/*.py
+    report/templates/*.html
 
 # [options.data_files]
 # snakemake = spacemake/snakemake/dropseq.smk