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update documentation
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tdayris committed Nov 28, 2023
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12 changes: 6 additions & 6 deletions README.md
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Expand Up @@ -34,18 +34,18 @@ The tools used in this pipeline are described [here](https://github.com/tdayris/

| 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) |
| Bowtie2-build | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-build](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/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) |
| Bowtie2-align | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-align](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/bowtie2/align.html) |
| Sambamba sort | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-sort](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/sambamba/sort.html) |

### Filtering

| Step | Meta-Wrapper | Wrapper |
| ---------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------- |
| Sambamba-view | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-view](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/sambamba/view.html) |
| Sambamba-markdup | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-markdup](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/sambamba/markdup.html) |
| Sambamba-index | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-index](https://snakemake-wrappers.readthedocs.io/en/v2.13.0/wrappers/sambamba/index.html) |
| Sambamba-view | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-view](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/sambamba/view.html) |
| Sambamba-markdup | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-markdup](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/sambamba/markdup.html) |
| Sambamba-index | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-index](https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/sambamba/index.html) |


### QC
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2 changes: 1 addition & 1 deletion workflow/report/fastp.rst
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Expand Up @@ -2,4 +2,4 @@ This HTML_ file contains Fastp_ quality reports for sample {{ snakemake.wildcard
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
.. _Fastp: https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/fastp.html
2 changes: 1 addition & 1 deletion workflow/report/multiqc.rst
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Expand Up @@ -2,5 +2,5 @@ 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
.. _Fastp: https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/fastp.html
.. _Picard: https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html
17 changes: 8 additions & 9 deletions workflow/report/workflows.rst
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Expand Up @@ -16,21 +16,20 @@ whole pipeline was powered by Snakemake_ [#snakemakepaper]_.
This pipeline is freely available on Github_, details about installation
usage, and resutls can be found on the `Snakemake workflow`_ page.


.. [#samtoolspaper] Li, Heng, et al. "The sequence alignment/map format and SAMtools." bioinformatics 25.16 (2009): 2078-2079.
.. [#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.
.. [#agatpaper] Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. (Version v0.7.0). Zenodo. https://www.doi.org/10.5281/zenodo.3552717
.. [#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.
.. [#agatpaper] Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. (Version v0.7.0). Zenodo. https://www.doi.org/10.5281/zenodo.3552717
.. [#samtoolspaper] Li, Heng, et al. "The sequence alignment/map format and SAMtools." bioinformatics 25.16 (2009): 2078-2079.
.. _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
.. _Sambamba: https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/sambamba.html
.. _Bowtie2: https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/bowtie2.html
.. _Fastp: https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/fastp.html
.. _Picard: https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/picard/collectmultiplemetrics.html
.. _MultiQC: https://snakemake-wrappers.readthedocs.io/en/v3.0.0/wrappers/multiqc.html
.. _Snakemake: https://snakemake.readthedocs.io
.. _Github: https://github.com/tdayris/fair_bowtie2_mapping
.. _`Snakemake workflow`: https://snakemake.github.io/snakemake-workflow-catalog?usage=tdayris/fair_bowtie2_mapping
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