Merge pull request #29 from cokelaer/main

update new apptainer for graphviz

README.rst

@@ -150,6 +150,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.17.1    * use new rulegraph / graphviz apptainer
 0.17.0    * fastp step changed to use sequana-wrappers. Slight change in 
             config file. The reverse and forward adapter options called
             rev and fwd have been dropped in favor of a single adapters option.

sequana_pipelines/rnaseq/config.yaml

@@ -22,6 +22,7 @@ apptainers:
   fastqc: "https://zenodo.org/record/7015004/files/fastqc_0.11.9-py3.img"
   fastp: "https://zenodo.org/record/7319782/files/fastp_0.23.2.img"
   igvtools: "https://zenodo.org/record/7022635/files/igvtools_2.12.0.img"
+  graphviz: "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
 
 # =========================================== Sections for the users
 

sequana_pipelines/rnaseq/rnaseq.rules

@@ -995,16 +995,28 @@ rule multiqc:
 # ========================================================== rulegraph
 
 rule rulegraph:
-    input: str(manager.snakefile)
+    input:
+        workflow.snakefile,
     output:
-        svg = ".sequana/rulegraph.svg"
+        "rulegraph/rulegraph.dot",
     params:
+        configname="config.yaml",
         mapper = {"multiqc": "../multiqc/multiqc_report.html"},
-        configname = "config.yaml"
     wrapper:
         f"{sequana_wrapper_branch}/wrappers/rulegraph"
 
 
+rule dot2svg:
+    input:
+        "rulegraph/rulegraph.dot"
+    output:
+        ".sequana/rulegraph.svg"
+    container:
+        config['apptainers']['graphviz']
+    shell:
+        """dot -Tsvg {input} -o {output}"""
+
+
 
 rule prepare_DGE_analysis:
     input: 

setup.py

@@ -5,7 +5,7 @@
 
 _MAJOR = 0
 _MINOR = 17
-_MICRO = 0
+_MICRO = 1
 version = "%d.%d.%d" % (_MAJOR, _MINOR, _MICRO)
 release = "%d.%d" % (_MAJOR, _MINOR)