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Commit da08ac95 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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# Results
Yours results are available in **./results/** directory, as follow:
_Some [temp] tagged files are removed by default, to save disk usage_
Results are available in **./results/** directry.
!!! tip
Files tagged as [temp] are removed by default, to save disk usage.
If you want to keep it, please edit configuration file.
!!! note
Files tree:
```shell
🧩 GeVarLi/
└── 📂 results/
......
# Résultats
Les résultats sont disponible dans le répertoire **./results/** , organisés comme ceci
!!! note
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.
!!! note
Arborescence des fichiers:
```shell
🧩 GeVarLi/
└── 📂 results/
├── 🧬 All_{REFERENCE}_consensus_sequences.fasta
├── 📊 All_{REFERENCE}_genome_coverages.tsv
├── 📊 All_{REFERENCE}_nextclade_lineages.tsv
├── 📊 All_{REFERENCE}_pangolin_lineages.tsv
├── 🌐 All_readsQC_reports.html
├── 📂 00_Quality_Control/
│ ├── 📂 fastq-screen/
│ │ ├── 🌐 {SAMPLE}_R{1/2}_screen.html
│ │ ├── 📈 {SAMPLE}_R{1/2}_screen.png
│ │ └── 📄 {SAMPLE}_R{1/2}_screen.txt
│ ├── 📂 fastqc/
│ │ ├── 🌐 {SAMPLE}_R{1/2}_fastqc.html
│ │ └── 📦 {SAMPLE}_R{1/2}_fastqc.zip
│ └── 📂 multiqc/
│ ├── 🌐 multiqc_report.html
│ └──📂 multiqc_data/
│ ├── 📝 multiqc.log
│ ├── 📄 multiqc_citations.txt
│ ├── 🌀 multiqc_data.json
│ ├── 📄 multiqc_fastq_screen.txt
│ ├── 📄 multiqc_fastqc.txt
│ ├── 📄 multiqc_general_stats.txt
| └── 📄 multiqc_sources.txt
├── 📂 01_Trimmidapt
│ ├── 📂 cutadapt/
│ │ └── 📦 {SAMPLE}_cutadapt-removed_R{1/2}.fastq.gz # [temp]
│ └── 📂 sickle/
│ ├── 📦 {SAMPLE}_sickle-trimmed_R{1/2}.fastq.gz # [temp]
│ └── 📦 {SAMPLE}_sickle-trimmed_SE.fastq.gz # [temp]
├── 📂 02_Mapping/
│ ├── 🧭 {SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.bam
│ ├── 🗂️ {SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.bam.bai
│ ├── 🧭 {SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.primerclipped.bam
│ ├── 🗂️ {SAMPLE}_{REFERENCE}_{ALIGNER}_mark-dup.primerclipped.bam.bai
│ ├── 🧭 {SAMPLE}_{ALIGNER}-mapped.sam # [temp]
│ ├── 🧭 {SAMPLE}_{REFERENCE}_{ALIGNER}_sorted-by-names.bam # [temp]
│ ├── 🧭 {SAMPLE}_{REFERENCE}_{ALIGNER}_fixed-mate.bam # [temp]
│ └── 🧭 {SAMPLE}_{REFERENCE}_{ALIGNER}_sorted.bam # [temp]
├── 📂 03_Coverage/
│ ├── 📊 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_coverage-stats.tsv
│ ├── 🛏️ {SAMPLE}_{REFERENCE}_{ALIGNER}_genome-cov.bed # [temp]
│ ├── 🛏️ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_min-cov-filt.bed # [temp]
│ └── 🛏️ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_low-cov-mask.bed # [temp]
├── 📂 04_Variants/
│ ├── 🧬 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_masked-ref.fasta
│ ├── 🗂️ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_masked-ref.fasta.fai
│ ├── 🧭 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_indel-qual.bam
│ ├── 🗂️ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_indel-qual.bai
│ ├── 🧮️ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-call.vcf
│ ├── 🧮️ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-filt.vcf
│ ├── 📦 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-filt.vcf.bgz # [temp]
│ └── 🗂️ {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_variant-filt.vcf.bgz.tbi # [temp]
├── 📂 05_Consensus/
│ └── 🧬 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_consensus.fasta
├── 📂 06_Lineages/
│ ├── 📊 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_nextclade-report.tsv
│ ├── 📊 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_pangolin-report.csv
│ └── 📂 {SAMPLE}_{REFERENCE}_{ALIGNER}_{MINCOV}_nextclade-all/
│ ├── 🧬 nextclade.aligned.fasta
│ ├── 📊 nextclade.csv
│ ├── 📊 nextclade.errors.csv
│ ├── 📊 nextclade.insertions.csv
│ ├── 🌀 nextclade.json
│ ├── 🌀 nextclade.ndjson
│ ├── 🌀 nextclade.auspice.json
│ └── 🧬 nextclade_{GENE}.translation.fasta
└── 📂 10_Reports/
├── ⚙️ config.log
├── 📝 settings.log
├── 🍜 gevarli-base_v.{VERSION}.yaml
├── 📂 conda_env/
│ └── 📄 {TOOLS}_v.{version}.yaml
├── 📂 files-summaries
├── 📂 graphs/
│ ├── 📈 {PIPELINE}_dag.{PNG/PDF}
│ ├── 📈 {PIPELINE}_filegraph.{PNG/PDF}
│ └── 📈 {PIPELINE}_rulegraph.{PNG/PDF}
└── 📂 tools-log/
├── 📂 awk/
├── 📂 {TOOL}/
```
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