Merge pull request #14 from cokelaer/main

switch to pyproject

.github/workflows/pypi.yml

@@ -11,20 +11,20 @@ jobs:
     runs-on: ubuntu-20.04
     steps:
     - uses: actions/checkout@main
-    - name: Set up Python 3.7
-      uses: actions/setup-python@v1
+    - name: Set up Python 3.8
+      uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
 
-    - name: Install package
+    - name: Install package 
       run: |
-          pip install build
+          pip install build poetry
 
     - name: Build source tarball
       run: |
           rm -rf dist;
-          python setup.py sdist
-
+          poetry build
+ 
     - name: Publish distribution to Test PyPI
       uses: pypa/gh-action-pypi-publish@release/v1
       with:

README.rst

@@ -116,6 +116,7 @@ Changelog
 ========= =======================================================================
 Version   Description
 ========= =======================================================================
+1.5.0     * Uses click and new sequana_pipetools, add multiqc
 1.4.0     * Implement demultiplexing of single cell ATAC seq data with 
             cellranger.
 1.3.1     * use sequana_wrappers version in the config file

pyproject.toml

@@ -0,0 +1,52 @@
+[build-system]
+requires = ["poetry-core>=1.0.0"]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "sequana-demultiplex"
+version = "1.5.0"
+description = "Pipeline that runs bcl2fastq and ease demultiplexing of Sequencing data"
+authors = ["Sequana Team"]
+license = "BSD-3"
+repository = "https://github.com/sequana/demultiplex"
+readme = "README.rst"
+keywords = ["bcl2fastq", "Illumina", "sequana", "base caller", "demultiplexing"]
+classifiers = [
+        "Development Status :: 5 - Production/Stable",
+        "Intended Audience :: Education",
+        "Intended Audience :: End Users/Desktop",
+        "Intended Audience :: Developers",
+        "Intended Audience :: Science/Research",
+        "License :: OSI Approved :: BSD License",
+        "Operating System :: POSIX :: Linux",
+        "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",
+]
+
+packages = [
+    {include = "sequana_pipelines"}
+]
+
+
+[tool.poetry.dependencies]
+python = ">=3.8,<4.0"
+sequana = ">=0.15.0"
+sequana_pipetools = ">=0.16.1"
+click-completion = "^0.5.2"
+
+
+[tool.poetry.scripts]
+sequana_demultiplex = "sequana_pipelines.demultiplex.main:main"
+
+
+[tool.poetry.group.dev.dependencies]
+black = "^23.7.0"
+pytest = "^7.4.0"
+mock = "^5.1.0"
+pytest-mock = "^3.11.1"
+pytest-cov = "^4.1.0"
+

requirements.txt

@@ -1,2 +1,2 @@
 sequana
-sequana_pipetools>=0.12.5
+sequana_pipetools>=0.16

sequana_pipelines/demultiplex/config.yaml

@@ -12,7 +12,7 @@
 #
 ##############################################################################
 
-sequana_wrappers: "v0.15.1"
+sequana_wrappers: "v23.11.18"
 
 #################################################################
 # general
@@ -34,6 +34,7 @@ general:
 apptainers:
   graphviz: "https://zenodo.org/record/7928262/files/graphviz_7.0.5.img"
   cellranger_atac: "https://zenodo.org/record/8423332/files/cellranger_atac_2.1.0.img"
+  multiqc: https://zenodo.org/record/10205070/files/multiqc_1.16.0.img
 
 ###################################################################################
 # bcl2fastq
@@ -62,3 +63,21 @@ cellranger_atac:
     options: ''
     resources:
         mem: 64G
+
+#############################################################################
+##   MultiQC aggregates results from bioinformatics analyses across many
+##   samples into a single report.
+##
+## :Parameters:
+##
+## - options: any options recognised by multiqc
+## - config_file: by default, we use sequana RNA-seq multiqc_config file.
+##       If you want your own multiqc, fill this entry
+multiqc:
+    options: -p -f
+    modules: bcl2fastq
+    input_directory: .
+    config_file: multiqc_config.yaml
+    resources:
+        mem: 8G
+

sequana_pipelines/demultiplex/demultiplex.rules

@@ -59,6 +59,7 @@ rule pipeline:
         "barcodes.png",
         "samples.png",
         "summary.png",
+        "multiqc/multiqc_report.html",
         ".sequana/rulegraph.svg",
 
 
@@ -155,6 +156,34 @@ rule plot_summary:
         s.to_summary_reads(output.summary)
 
 
+
+# ========================================================== multiqc
+multiqc_params_options = config['multiqc']['options']
+if manager.config.multiqc.config_file:
+    multiqc_params_options += f" -c {manager.config.multiqc.config_file}"
+
+rule multiqc:
+    input:
+        "Stats/Stats.json",
+        "Stats/summary.txt",
+    output:
+       "multiqc/multiqc_report.html"
+    params:
+        options=multiqc_params_options,
+        input_directory=config['multiqc']['input_directory'],
+        config_file=config['multiqc']['config_file'],
+        modules=config['multiqc']['modules']
+    log:
+        "multiqc/multiqc.log"
+    resources:
+        **config["multiqc"]["resources"]
+    container:
+        config["apptainers"]["multiqc"]
+    wrapper:
+       f"{manager.wrappers}/wrappers/multiqc"
+
+
+
 rule rulegraph:
     input:
         workflow.snakefile
@@ -183,18 +212,22 @@ localrules: rulegraph
 
 onsuccess:
     shell("chmod -R g+w .")
+
+    from sequana_pipelines import demultiplex
+    from sequana.modules_report.summary import SequanaReport
+
     manager.teardown(extra_dirs_to_remove=["_Temp"])
+    manager.clean_multiqc(rules.multiqc.output[0])
 
-    from sequana.modules_report.summary import SummaryModule2
 
-    image1 = SummaryModule2.png_to_embedded_png("dummy", "barcodes.png",
+    image1 = SequanaReport.png_to_embedded_png("dummy", "barcodes.png",
                 style="text-align:center; width:60%; height:40%", 
                 alt="barcodes")
 
-    image2 = SummaryModule2.png_to_embedded_png("dummy", "summary.png",
+    image2 = SequanaReport.png_to_embedded_png("dummy", "summary.png",
                 style="width:60%; height:40%", alt="summary")
 
-    image3 = SummaryModule2.png_to_embedded_png("dummy", "samples.png",
+    image3 = SequanaReport.png_to_embedded_png("dummy", "samples.png",
                 style="width:60%; height:40%", alt="sample")
 
 
@@ -218,17 +251,11 @@ The following image is similar. Instead of showing the index, we show here the n
 
 </div>""".format(image1, image2, image3)
 
-    from sequana_pipelines import demultiplex
-    data = {
-            "name": manager.name,
-            "stats": "stats.txt", 
-            "rulegraph": ".sequana/rulegraph.svg",
-            "pipeline_version": demultiplex.version
-            }
-    s = SummaryModule2(data, intro=intro)
+
+    data = manager.getmetadata()
+    s = SequanaReport(data, intro=intro)
+
 
 onerror:
-    from sequana_pipetools.errors import PipeError
-    p = PipeError("demultiplex")
-    p.status()
+    manager.onerror()