Merge pull request #7 from cokelaer/main

update pipeline to use latest apptainers

.github/workflows/apptainer.yml

@@ -59,4 +59,3 @@ jobs:
 
 
 
-

.github/workflows/main.yml

@@ -8,15 +8,15 @@ on:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 * * SUN'
+    - cron: '0 0 2 * *'
 
 jobs:
   build-linux:
     runs-on: ubuntu-latest
     strategy:
       max-parallel: 5
       matrix:
-        python: [3.7, 3.8, 3.9]
+        python: [3.8, 3.9, '3.10']
       fail-fast: false
 
 

README.rst

@@ -104,6 +104,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+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
 0.11.1    * Fix config file (removing hard-coded path)

sequana_pipelines/ribofinder/config.yaml

@@ -45,6 +45,7 @@ apptainers:
     pigz: "https://zenodo.org/record/7346805/files/pigz_2.4.0.img"
     bedtools: "https://zenodo.org/record/7346774/files/bedtools_2.30.0.img"
     samtools: "https://zenodo.org/record/7215278/files/samtools_1.15.0.img"
+    graphviz:  "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
 
 #############################################################################
 # bowtie1_mapping_rna used to align reads against ribosomal RNA

sequana_pipelines/ribofinder/ribofinder.rules

@@ -26,7 +26,7 @@ from sequana.gff3 import GFF3
 configfile: "config.yaml"
 
 manager = PipelineManager("ribofinder", config)
-
+sequana_wrapper_branch = "main"
 
 
 rule pipeline:
@@ -135,7 +135,7 @@ rule bowtie1_indexing:
     container:
         config['apptainers']['sequana_ribofinder']
     wrapper:
-        "main/wrappers/bowtie1/build"
+        f"{sequana_wrapper_branch}/wrappers/bowtie1/build"
 
 
 
@@ -177,7 +177,7 @@ rule bowtie1_mapping_rna:
     container:
         config['apptainers']['sequana_ribofinder']
     wrapper:
-        "main/wrappers/bowtie1/align"
+        f"{sequana_wrapper_branch}/wrappers/bowtie1/align"
 
 
 # ======================================================== Fix bowtie log
@@ -277,12 +277,46 @@ rule bam_indexing:
 #
 sequana_multiqc_input = expand("{sample}/bowtie1/{sample}.sorted.bam.bai", sample=sorted(manager.samples))
 sequana_multiqc_input += ["logs/fix_bowtie1_log"]
-include: sm.modules["multiqc/2.0"]
+
+
+rule multiqc:
+    input:
+        sequana_multiqc_input
+    output:
+       "multiqc/multiqc_report.html"
+    params:
+        options=config['multiqc']['options'],
+        input_directory=config['multiqc']['input_directory'],
+        config_file=config['multiqc']['config_file'],
+        modules=config['multiqc']['modules']
+    log:
+        "multiqc/multiqc.log"
+    wrapper:
+       f"{sequana_wrapper_branch}/wrappers/multiqc"
+
 
 # ========================================================== rulegraph
-#
-sequana_rulegraph_mapper = {"multiqc": "../multiqc/multiqc_report.html"}
-include: sm.modules['rulegraph']
+rule rulegraph:
+    input: str(manager.snakefile)
+    output:
+        svg = "rulegraph/rulegraph.dot"
+    params:
+        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}"""
+
 
 
 

setup.py

@@ -3,8 +3,8 @@
 from setuptools.command.install import install
 import subprocess
 
-_MAJOR               = 0
-_MINOR               = 13
+_MAJOR               = 1
+_MINOR               = 0
 _MICRO               = 0
 version              = '%d.%d.%d' % (_MAJOR, _MINOR, _MICRO)
 release              = '%d.%d' % (_MAJOR, _MINOR)
@@ -25,9 +25,9 @@
           'Intended Audience :: Science/Research',
           'License :: OSI Approved :: BSD License',
           'Operating System :: OS Independent',
-          'Programming Language :: Python :: 3.7',
           'Programming Language :: Python :: 3.8',
           'Programming Language :: Python :: 3.9',
+          'Programming Language :: Python :: 3.10',
           'Topic :: Software Development :: Libraries :: Python Modules',
           'Topic :: Scientific/Engineering :: Bio-Informatics',
           'Topic :: Scientific/Engineering :: Information Analysis',