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Commit 669e6993 authored by nicolas.fernandez_ird.fr's avatar nicolas.fernandez_ird.fr :shinto_shrine:
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Doc: Add french results

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# Features and tools # Features and tools
## Workflow management ## Workflow management
- Workflow ......................... Snakemake - Workflow _ _ _ _ _ _ _ _ _ _ _ _ _ Snakemake
- Environments ..................... Miniforge _(Conda)_ - Environments _ _ _ _ _ _ _ _ _ _ _ Miniforge _(Conda)_
## Reads quality control ## Reads quality control
- Contamination checking ........... Fastq-Screen - Contamination checking _ _ _ _ _ _ Fastq-Screen
- Reads qualities metrics .......... FastQC - Reads qualities metrics _ _ _ _ _ FastQC
- HTML reporting ................... MultiQC - HTML reporting _ _ _ _ _ _ _ _ _ _ MultiQC
## Reads cleaning ## Reads cleaning
- Illumina adpters trimming ........ Cutadapt - Illumina adpters trimming _ _ _ _ Cutadapt
- Amplicon primers trimming ........ Cutadapt _('hard-clipping')_ - Amplicon primers trimming _ _ _ _ Cutadapt _('hard-clipping')_
- Reads quality trimming ........... Sickle-trim - Reads quality trimming _ _ _ _ _ _ Sickle-trim
## Reads mapping ## Reads mapping
- Indexing genomes ................. BWA _(or minimap2, or bowtie2)_ - Indexing genomes ................. BWA _(or minimap2, or bowtie2)_
......
...@@ -3,18 +3,16 @@ ...@@ -3,18 +3,16 @@
Results are available in **./results/** directry. Results are available in **./results/** directry.
!!! tip !!! tip
Files tagged as [temp] are removed by default, to save disk usage. Files tagged as **[temp]** are removed by default, to save disk usage.
If you want to keep it, please edit configuration file. If you want to keep them, please edit the **configuration** file.
!!! note !!! note
Files tree: **Files tree**
```shell 🧩 GeVarLi/
🧩 GeVarLi/ └── 📂 results/
└── 📂 results/ ├── 🧬 All_{REFERENCE}_consensus_sequences.fasta
├── 🧬 All_{REFERENCE}_consensus_sequences.fasta ├── 📊 All_{REFERENCE}_genome_coverages.tsv
├── 📊 All_{REFERENCE}_genome_coverages.tsv ├── 📊 All_{REFERENCE}_nextclade_lineages.tsv
├── 📊 All_{REFERENCE}_nextclade_lineages.tsv
├── 📊 All_{REFERENCE}_pangolin_lineages.tsv ├── 📊 All_{REFERENCE}_pangolin_lineages.tsv
├── 🌐 All_readsQC_reports.html ├── 🌐 All_readsQC_reports.html
├── 📂 00_Quality_Control/ ├── 📂 00_Quality_Control/
...@@ -92,4 +90,3 @@ Results are available in **./results/** directry. ...@@ -92,4 +90,3 @@ Results are available in **./results/** directry.
└── 📂 tools-log/ └── 📂 tools-log/
├── 📂 awk/ ├── 📂 awk/
├── 📂 {TOOL}/ ├── 📂 {TOOL}/
```
...@@ -3,15 +3,13 @@ ...@@ -3,15 +3,13 @@
Les résultats sont disponible dans le répertoire **./results/** , organisés comme ceci Les résultats sont disponible dans le répertoire **./results/** , organisés comme ceci
!!! note !!! note
Les fichiers étiqueté comme [temp] sont supprimés par défaut, afin de préserver l'espace disque. Les fichiers étiqueté comme **[temp]** sont supprimés par défaut, afin de préserver l'espace disque.
Si vous souhaiter les conserver, veuiller éditer le fichier de configuration. Si vous souhaiter les conserver, veuiller éditer le fichier de **configuration**.
!!! note !!! note
Arborescence des fichiers: **Arborescence des fichiers**
```shell
🧩 GeVarLi/ 🧩 GeVarLi/
└── 📂 results/ └── 📂 results/
├── 🧬 All_{REFERENCE}_consensus_sequences.fasta ├── 🧬 All_{REFERENCE}_consensus_sequences.fasta
......
...@@ -121,9 +121,9 @@ nav: ...@@ -121,9 +121,9 @@ nav:
- Acknowledgements: en/pages/acknowledgements.md - Acknowledgements: en/pages/acknowledgements.md
- Accueil (fr): - Accueil (fr):
- À propos: fr/index.md - À propos: fr/index.md
- Caractéristiques: fr/pages/features.md - Fonctionnalités: fr/pages/features.md
- Installations: fr/pages/installations.md - Installations: fr/pages/installations.md
- Configuration: fr/pages/setup.md - Configuration: fr/pages/configuration.md
- Utilisation: fr/pages/usage.md - Utilisation: fr/pages/usage.md
- Résultats: fr/pages/results.md - Résultats: fr/pages/results.md
- Glossaire: fr/pages/glossary.md - Glossaire: fr/pages/glossary.md
......
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