Merge pull request #21 from cokelaer/main

Fix CI and typo in onerror section

.github/workflows/apptainer.yml

@@ -49,6 +49,7 @@ jobs:
     - name: install package itself
       run: |
          pip install .
+         pip install "pulp==2.7.0" --no-deps
 
     - name: testing
       run: |

.github/workflows/main.yml

@@ -9,7 +9,7 @@ on:
   pull_request:
     branches-ignore: []
   schedule:
-    - cron: '0 0 1 * *'
+    - cron: '0 0 8 * *'
 
 jobs:
   build-linux:
@@ -37,11 +37,12 @@ jobs:
           extra-specs: |
             python=${{ matrix.python }}
 
-
     - name: install package itself
       shell: bash -l {0}
       run: |
         pip install .
+        pip install "pulp==2.7.0" --no-deps
+
 
     - name: Install dependencies
       shell: bash -l {0}

README.rst

@@ -132,6 +132,7 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.8.2     * Fix the onerror typo in the pipeline, fix CI.
 1.8.1     * update __init__ (version)
 1.8.0     * uses pyproject instead of setuptools
           * uses click instead of argparse and newest sequana_pipetools 

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-fastqc"
-version = "1.8.1"
+version = "1.8.2"
 description = "A multi-sample fastqc pipeline from Sequana project"
 authors = ["Sequana Team"]
 license = "BSD-3"

sequana_pipelines/fastqc/config.yaml

@@ -32,6 +32,8 @@ apptainers:
 #
 # Choose one of the standard method to perform QC of your fastq data
 #
+# method_choice__ = ["fastqc", "falco"]
+#
 general:
     method_choice: fastqc
 

sequana_pipelines/fastqc/fastqc.rules

@@ -256,13 +256,15 @@ localrules: rulegraph
 
 onsuccess:
 
+    from sequana.modules_report.summary import SequanaReport
+    from sequana import logger
+    logger.setLevel("INFO")
+
     # Create the tree.html file with all fastqc reports
     hh = HTMLDirectory(".", pattern="fastqc.html")
     with open("tree.html", "w") as fout:
         fout.write(hh.get_html())
 
-    from sequana import logger
-    logger.setLevel("INFO")
 
     # This should create the stats plot and the Makefile
     manager.teardown()
@@ -323,22 +325,13 @@ onsuccess:
     htmltable2 = datatable.create_datatable(style="width: 20%; float:left" )
 
 
-    from sequana.modules_report.summary import SummaryModule2
-    from sequana_pipelines import fastqc
-    data = {
-            "name": manager.name,
-            "rulegraph": ".sequana/rulegraph.svg",
-            "stats": "stats.txt",
-            "pipeline_version": fastqc.version
-
-         }
 
     # Here the is main HTML page report
     contents = f"""<h2> General information</h2>
                   <div style="float:left; width:30%">{js2} {htmltable2}</div>
                """
 
-    image = SummaryModule2.png_to_embedded_png("dummy", "outputs/summary.png", 
+    image = SequanaReport.png_to_embedded_png("dummy", "outputs/summary.png", 
                 style="width:80%; height:40%")
 
     contents += f"""<div style="float:right; width:65%">
@@ -359,12 +352,13 @@ onsuccess:
     contents += hh.get_html()
 
 
-    s = SummaryModule2(data, intro=contents)
+    data = manager.getmetadata() 
+    s = SequanaReport(data, intro=contents)
 
     # finally, some cleanup
     shell("rm -rf rulegraph")   # embedded in report
     shell("chmod -R g+w .")
 
 onerror:
-    manager.error_status()
+    manager.onerror()