Merge pull request #8 from cokelaer/main

Use sequana_wrappers from the config file

README.rst

@@ -109,6 +109,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.0.1     * add sequana_wrappers in the config/pipeline
 1.0.0     * use graphviz apptainer and latest wrappers
 0.13.0    * add  final apptainers and update CI actions
 0.12.0    * set singularity containers

requirements.txt

@@ -1,2 +1,2 @@
 sequana>=0.14.1
-sequana_pipetools>=0.9.2
+sequana_pipetools>=0.12.5

sequana_pipelines/ribofinder/config.yaml

@@ -7,6 +7,7 @@
 # If input_directory provided, use it otherwise if input_pattern provided,
 # use it, otherwise use input_samples.
 # ============================================================================
+sequana_wrappers: "v0.15.1"
 input_directory:
 input_readtag: _R[12]_
 input_pattern: '*fastq.gz'

sequana_pipelines/ribofinder/ribofinder.rules

@@ -18,15 +18,12 @@ from collections import Counter
 
 
 from sequana_pipetools import PipelineManager
-from sequana_pipetools import snaketools as sm
-from sequana import logger as log
-
 from sequana.gff3 import GFF3
+from sequana import logger as log
 
 configfile: "config.yaml"
 
 manager = PipelineManager("ribofinder", config)
-sequana_wrapper_branch = "main"
 
 
 rule pipeline:
@@ -135,7 +132,7 @@ rule bowtie1_indexing:
     container:
         config['apptainers']['sequana_ribofinder']
     wrapper:
-        f"{sequana_wrapper_branch}/wrappers/bowtie1/build"
+        f"{manager.wrappers}/wrappers/bowtie1/build"
 
 
 
@@ -177,7 +174,7 @@ rule bowtie1_mapping_rna:
     container:
         config['apptainers']['sequana_ribofinder']
     wrapper:
-        f"{sequana_wrapper_branch}/wrappers/bowtie1/align"
+        f"{manager.wrappers}/wrappers/bowtie1/align"
 
 
 # ======================================================== Fix bowtie log
@@ -292,7 +289,7 @@ rule multiqc:
     log:
         "multiqc/multiqc.log"
     wrapper:
-       f"{sequana_wrapper_branch}/wrappers/multiqc"
+       f"{manager.wrappers}/wrappers/multiqc"
 
 
 # ========================================================== rulegraph
@@ -304,7 +301,7 @@ rule rulegraph:
         mapper = {"multiqc": "../multiqc/multiqc_report.html"},
         configname = "config.yaml"
     wrapper:
-        f"{sequana_wrapper_branch}/wrappers/rulegraph"
+        f"{manager.wrappers}/wrappers/rulegraph"
 
 
 rule dot2svg:

setup.py

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