Add a multiqc report and containerize the trimming

README.rst

@@ -93,6 +93,12 @@ ChangeLog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+1.3.0     * add a multiqc report aggregating the FastQC and cutadapt results
+          * the trimming is now a shell rule running in the cutadapt
+            container (it was a python rule using the local installation)
+          * add the missing log files so that the pipeline monitor reports
+            the correct elapsed times
+          * require sequana >=0.24.1
 1.2.0     * fix --skip-phix-removal and --disable-trimming, which both ended
             in a NameError
           * compute the FastQ statistics of R2 as well (R1 only before)

environment.yml

@@ -10,6 +10,7 @@ dependencies:
 - fastqc
 - sambamba
 - graphviz
+- multiqc
 - pulp>=2.8
 - pip:
   - sequana

pyproject.toml

@@ -4,13 +4,13 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "sequana-quality-control"
-version = "1.2.0"
+version = "1.3.0"
 description = "Quality control pipeline for NGS data (phix removal, adapter trimming, FastQC)"
 authors = ["Sequana Team"]
 license = "BSD-3"
 repository = "https://github.com/sequana/quality_control"
 readme = "README.rst"
-keywords = ["snakemake", "NGS", "sequana", "fastqc", "cutadapt"]
+keywords = ["snakemake", "NGS", "sequana", "fastqc", "cutadapt", "multiqc"]
 classifiers = [
         "Development Status :: 5 - Production/Stable",
         "Intended Audience :: Education",
@@ -35,7 +35,7 @@ packages = [
 
 [tool.poetry.dependencies]
 python = ">=3.9,<4.0"
-sequana = ">=0.18.0"
+sequana = ">=0.24.1"
 sequana_pipetools = ">=1.1.1"
 sequana-wrappers = ">=26.4.16"
 snakemake = ">=7.32"

sequana_pipelines/quality_control/config.yaml

@@ -13,6 +13,8 @@ reference_file: phiX174.fa
 
 
 apptainers:
+    cutadapt: https://zenodo.org/record/18834062/files/cutadapt_4.6.0.img
+    multiqc: https://zenodo.org/record/10155626/files/multiqc_1.17.0.img
     pigz: https://zenodo.org/record/7346805/files/pigz_2.4.0.img
     fastqc: https://zenodo.org/record/7015004/files/fastqc_0.11.9-py3.img
     sequana_minimal: https://zenodo.org/record/19127803/files/sequana_minimal_26.3.19.img
@@ -109,3 +111,21 @@ fastqc:
 
 fastq_stats:
     max_reads: 500000
+
+
+#############################################################################
+# MultiQC aggregates the FastQC and cutadapt reports in a single HTML file
+#
+# :Parameters:
+#
+# - do: if unchecked, this rule is ignored
+# - options: any options recognised by multiqc
+# - input_directory: where to look for the reports
+# - modules: the multiqc modules to use (space separated)
+# - config_file: an optional multiqc configuration file
+multiqc:
+    do: true
+    options: -p -f
+    input_directory: '.'
+    modules: fastqc cutadapt
+    config_file: