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documentation update
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tdayris committed Mar 29, 2024
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8 changes: 8 additions & 0 deletions CHANGELOG.md
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# 3.3.1

## Features:

* fair_genome_indexer update to 3.4.0
* fair_fastqc_multiqc update to 2.2.3
* snakemake-wrappers update to 3.7.0

# 3.3.0

## Featues:
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20 changes: 10 additions & 10 deletions README.md
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Expand Up @@ -28,10 +28,10 @@ See [`fair_fastqc_multiqc`](https://github.com/tdayris/fair_fastqc_multiqc/) do

| Step | Meta-Wrapper | Wrapper |
| ------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------- |
| Bowtie2-build | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-build](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/bowtie2/build.html) |
| Fastp | | [fastp](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/fastp.html) |
| Bowtie2-align | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-align](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/bowtie2/align.html) |
| Sambamba sort | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/meta-wrappers/bowtie2_sambamba.html) | [sambamba-sort](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/sambamba/sort.html) |
| Bowtie2-build | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-build](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/bowtie2/build.html) |
| Fastp | | [fastp](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/fastp.html) |
| Bowtie2-align | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/meta-wrappers/bowtie2_sambamba.html) | [bowtie2-align](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/bowtie2/align.html) |
| Sambamba sort | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-sort](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/sambamba/sort.html) |

```
┌───────────────────────────┐ ┌─────────────────────────┐
Expand All @@ -54,9 +54,9 @@ See [`fair_fastqc_multiqc`](https://github.com/tdayris/fair_fastqc_multiqc/) do

| Step | Meta-Wrapper | Wrapper |
| ---------------- | ------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------- |
| Sambamba-view | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/meta-wrappers/bowtie2_sambamba.html) | [sambamba-view](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/sambamba/view.html) |
| Sambamba-markdup | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/meta-wrappers/bowtie2_sambamba.html) | [sambamba-markdup](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/sambamba/markdup.html) |
| Sambamba-index | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/meta-wrappers/bowtie2_sambamba.html) | [sambamba-index](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/sambamba/index.html) |
| Sambamba-view | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-view](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/sambamba/view.html) |
| Sambamba-markdup | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-markdup](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/sambamba/markdup.html) |
| Sambamba-index | [bowtie2-sambamba meta-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/meta-wrappers/bowtie2_sambamba.html) | [sambamba-index](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/sambamba/index.html) |

```
┌──────────────────────────┐
Expand All @@ -83,9 +83,9 @@ See [`fair_fastqc_multiqc`](https://github.com/tdayris/fair_fastqc_multiqc/) do

| Step | Wrapper |
| -------- | -------------------------------------------------------------------------------------------------------------------------------- |
| Picard | [picard-collectmultiplemetrics](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/picard/collectmultiplemetrics.html) |
| Samtools | [samtools-stats](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/samtools/stats.html) |
| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.4.1/wrappers/multiqc.html) |
| Picard | [picard-collectmultiplemetrics](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/picard/collectmultiplemetrics.html) |
| Samtools | [samtools-stats](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/samtools/stats.html) |
| MultiQC | [multiqc-wrapper](https://snakemake-wrappers.readthedocs.io/en/v3.7.0/wrappers/multiqc.html) |

```
┌──────────────────────┐ ┌─────────────────────┐ ┌─────────────────────────┐
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