From f7b9b723419a24881ce2657dc8361d8d27e94059 Mon Sep 17 00:00:00 2001 From: tdayris Date: Tue, 5 Dec 2023 10:11:36 +0100 Subject: [PATCH] documentation update --- README.md | 11 ++++++----- workflow/report/material_methods.rst | 5 +++-- 2 files changed, 9 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 8cb9188..804aeb5 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ A complete description of the results can be found here in [workflow reports](ht ## Material and Methods -The tools used in this pipeline are described [here](https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/report/workflows.rst) textually. Web-links are available below: +The tools used in this pipeline are described [here](https://github.com/tdayris/fair_bowtie2_mapping/blob/main/workflow/report/material_methods.rst) textually. Web-links are available below: ![workflow_rulegraph](dag.png) @@ -50,7 +50,8 @@ The tools used in this pipeline are described [here](https://github.com/tdayris/ ### QC -| Step | Wrapper | -| ------- | -------------------------------------------------------------------------------------------------------------------------------- | -| Picard | [picard-collectmultiplemetrics](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html) | -| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/multiqc.html) | \ No newline at end of file +| Step | Wrapper | +| -------- | -------------------------------------------------------------------------------------------------------------------------------- | +| Picard | [picard-collectmultiplemetrics](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/picard/collectmultiplemetrics.html) | +| Samtools | [samtools-stats](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/samtools/stats.html) | +| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/multiqc.html) | \ No newline at end of file diff --git a/workflow/report/material_methods.rst b/workflow/report/material_methods.rst index 33d6df4..cef82e2 100644 --- a/workflow/report/material_methods.rst +++ b/workflow/report/material_methods.rst @@ -9,8 +9,9 @@ genome annotation files. 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 +controls were done on cleaned, sorted, deduplicated aligned reads using +Picard_ [#picardpaper]_ and Samtools_ [#samtoolspaper]_. 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_, details about installation