dev: report addition

.github/workflows/main.yaml

@@ -48,4 +48,10 @@ jobs:
       with:
         directory: .test
         snakefile: workflow/Snakefile
-        args: "--use-conda --use-singularity --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
+        args: "--use-conda --use-singularity --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
+    - name: Test report
+      uses: snakemake/snakemake-github-action@v1.22.0
+      with:
+        directory: .test
+        snakefile: workflow/Snakefile
+        args: "--use-conda --use-singularity --cores 2 --report report.zip"

.snakemake-workflow-catalog.yaml

@@ -6,6 +6,6 @@ usage:
     flags: FAIR Bowtie2 Sambamba Snakemake Ensembl
   software-stack-deployment:
     conda: true
-    singularity: false
-    singularity+conda: false
-  report: false
+    singularity: true
+    singularity+conda: true
+  report: true

.test/genomes.csv

@@ -0,0 +1,2 @@
+species,build,release
+saccharomyces_cerevisiae,R64-1-1,110

.test/makefile

@@ -18,9 +18,14 @@ snakefiles := \
 
 
 .PHONY: all
-all: pipeline.txt
+all: report.txt
 
 
+report.txt: pipeline.txt
+	mamba activate test-snakemake-wrappers && \
+	snakemake -s ../workflow/Snakefile \
+		--report report.html
+
 
 pipeline.txt: format.txt linter.txt
 	mamba activate test-snakemake-wrappers && \

CHANGELOG.md

@@ -1,3 +1,13 @@
+# 2.1.0
+
+## Features:
+
+* Add report texts
+
+## Documentation
+
+* Fastp citation
+
 # 2.0.0
 
 ## Features:

README.md

@@ -21,9 +21,10 @@ The usage of this workflow is described in the [Snakemake workflow catalog](http
 
 ### Bowtie2 Mapping
 
-| Step          | Meta-Wrapper                                                                                                   | Wrapper                                                                                           |
+| Step          | Meta-Wrapper                                                                                                              | Wrapper                                                                                           |
 | ------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
 | Bowtie2-build | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-build](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/bowtie2/build.html) |
+| Fastp         |                                                                                                                           | [fastp](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/fastp.html)                  |
 | Bowtie2-align | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-align](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/bowtie2/align.html) |
 | Sambamba sort | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-sort](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/sambamba/sort.html) |
 

workflow/report/multiqc.rst

@@ -0,0 +1,6 @@
+This HTML_ file contains quality reports of both Fastp_ and Picard_.
+It is a stand-alone file, and can be opened in your favorite web-browser.
+
+.. _HTML: https://en.wikipedia.org/wiki/HTML
+.. _Fastp: https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/fastp.html
+.. _Picard: https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html

workflow/report/workflows.rst

@@ -0,0 +1,31 @@
+Matierial and methods
+=====================
+
+Raw fastq files were trimmed using Fastp_ [#fastppaper]_ . Cleaned reads were aligned 
+over indexed Ensembl genome with Bowtie2_ [#bowtie2paper]_. Sambamba_ [#sambambapaper]_ 
+was used to sort, filter, mark duplicates, and compress aligned reads. Quality 
+controls were done using Picard_ [#picardpaper]_. Quality repord produced during both
+trimming and mapping steps have been aggregated with MultiQC_ [#multiqcpaper]_. The 
+whole pipeline was powered by Snakemake_ [#snakemakepaper]_.
+
+This pipeline is freely available on Github_ 
+
+.. [#fastppaper] Chen, Shifu, et al. "fastp: an ultra-fast all-in-one FASTQ preprocessor." Bioinformatics 34.17 (2018): i884-i890.
+.. [#bowtie2paper] Langmead, Ben, and Steven L. Salzberg. "Fast gapped-read alignment with Bowtie 2." Nature methods 9.4 (2012): 357-359.
+.. [#sambambapaper] Tarasov, Artem, et al. "Sambamba: fast processing of NGS alignment formats." Bioinformatics 31.12 (2015): 2032-2034.
+.. [#picardpaper] McKenna, Aaron, et al. "The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data." Genome research 20.9 (2010): 1297-1303.
+.. [#multiqcpaper] Ewels, Philip, et al. "MultiQC: summarize analysis results for multiple tools and samples in a single report." Bioinformatics 32.19 (2016): 3047-3048.
+.. [#snakemakepaper] Köster, Johannes, and Sven Rahmann. "Snakemake—a scalable bioinformatics workflow engine." Bioinformatics 28.19 (2012): 2520-2522.
+
+.. _Sambamba: https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/sambamba.html
+.. _Bowtie2: https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/bowtie2.html
+.. _Fastp: https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/fastp.html
+.. _Picard: https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/picard/collectmultiplemetrics.html
+.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/multiqc.html
+.. _Snakemake: https://snakemake.readthedocs.io
+.. _Github: https://github.com/tdayris/fair_bowtie2_mapping
+
+:Authors:
+    Thibault Dayris
+
+:Version: 2.1.0 of 11/22/2023

workflow/rules/common.smk

@@ -60,6 +60,7 @@ snakemake.utils.validate(genomes, "../schemas/genomes.schema.yaml")
 
 snakemake_wrappers_version: str = "v2.13.0"
 
+report: "../report/workflows.rst"
 
 wildcard_constraints:
     sample=r"|".join(samples.sample_id),

workflow/rules/multiqc.smk

@@ -2,7 +2,11 @@ rule multiqc_report:
     input:
         unpack(get_multiqc_report_input),
     output:
-        "results/QC/MultiQC.html",
+        report(
+            "results/QC/MultiQC.html",
+            caption="../report/multiqc.rst",
+            category="Quality Controls",
+        ),
         "results/QC/MultiQC_data.zip",
     params:
         extra="--zip-data-dir",