documentation update

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) |
+| 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)                                     |

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