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Added ToulligQC in raw read QC step #287

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Added ToulligQC in raw read QC step #287

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a1349c2
ADD: added ToulligQC module to pipeline Nanoseq
Salome-Brunon Apr 9, 2024
f4ff2f2
ADD: added documentation about ToulligQC
Salome-Brunon Nov 22, 2024
d6844f2
UDPATE: upgraded version
Salome-Brunon Nov 22, 2024
336af63
FIX: resolve conflicts
Salome-Brunon Nov 22, 2024
f1bc1d4
FIX: ran prettier on modules.json
Salome-Brunon Nov 22, 2024
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2 changes: 2 additions & 0 deletions CITATIONS.md
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Expand Up @@ -82,6 +82,8 @@

> Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. Transcriptome assembly from long-read RNA-seq alignments with StringTie2 Genome Biol. 2019 Dec 16;20(1):278. doi: 10.1186/s13059-019-1910-1. PubMed PMID: 31842956; PubMed Central PMCID: PMC6912988.

- [ToulligQC](https://github.com/GenomiqueENS/toulligQC)

- [UCSC tools](https://www.ncbi.nlm.nih.gov/pubmed/20639541/)

> Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D. BigWig and BigBed: enabling browsing of large distributed datasets. Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17. PubMed PMID: 20639541; PubMed Central PMCID: PMC2922891.
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -25,7 +25,7 @@ On release, automated continuous integration tests run the pipeline on a [full-s

1. Demultiplexing ([`qcat`](https://github.com/nanoporetech/qcat); _optional_)
2. Raw read cleaning ([NanoLyse](https://github.com/wdecoster/nanolyse); _optional_)
3. Raw read QC ([`NanoPlot`](https://github.com/wdecoster/NanoPlot), [`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
3. Raw read QC ([`NanoPlot`](https://github.com/wdecoster/NanoPlot), [`ToulligQC`](https://github.com/GenomiqueENS/toulligQC), [`FastQC`](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
4. Alignment ([`GraphMap2`](https://github.com/lbcb-sci/graphmap2) or [`minimap2`](https://github.com/lh3/minimap2))
- Both aligners are capable of performing unspliced and spliced alignment. Sensible defaults will be applied automatically based on a combination of the input data and user-specified parameters
- Each sample can be mapped to its own reference genome if multiplexed in this way
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12 changes: 12 additions & 0 deletions conf/modules.config
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Expand Up @@ -94,6 +94,18 @@ if (!params.skip_qc) {
}
}
}
if (!params.skip_toulligqc) {
process {
withName: TOULLIGQC {
publishDir = [
path: { "${params.outdir}/toulligqc" },
mode: 'copy',
enabled: true,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
}
}
if (!params.skip_fastqc) {
process {
withName: FASTQC {
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Binary file added docs/images/toulligqc_report_barcodes.png
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9 changes: 8 additions & 1 deletion docs/output.md
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Expand Up @@ -54,11 +54,14 @@ If you would like to run NanoLyse on the raw FASTQ files you can provide `--run_
- `nanoplot/fastq/<SAMPLE>/`: directory with various `*.html` files containing QC metrics and plots.
- `fastqc/<SAMPLE>_fastqc.html`: _FastQC_ `*.html` file for each sample.
- `fastqc/<SAMPLE>_fastqc.zip`: _FastQC_ `*.zip` file for each sample.
- `toulligqc/<SAMPLE>_ToulligQC-report-<date>/report.html`: _ToulligQC_ `*.html` browser-viewable report that contains all the figures in a single location for each sample.
- `toulligqc/<SAMPLE>_ToulligQC-report-<date>/report.data`: A log file containing information about ToulligQC execution, environment variables and full statistics.
- `toulligqc/<SAMPLE>_ToulligQC-report-<date>/images/*`: This is folder containing all the individual images produced by ToulligQC.

</details>

_Documentation_:
[NanoPlot](https://github.com/wdecoster/NanoPlot), [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/)
[NanoPlot](https://github.com/wdecoster/NanoPlot), [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/), [ToulligQC](https://github.com/GenomiqueENS/toulligQC)

_Description_:
_NanoPlot_ can be used to produce general quality metrics from the per barcode FASTQ files generated by a basecaller e.g. quality score distribution, read lengths, and other general stats.
Expand All @@ -67,6 +70,10 @@ _NanoPlot_ can be used to produce general quality metrics from the per barcode F

_FastQC_ can give general quality metrics about your reads. It can provide information about the quality score distribution across your reads, and the per-base sequence content (%A/C/G/T). You can also generate information about adapter contamination and other over-represented sequences.

_ToulligQC_ is dedicated to the QC analyses of Oxford Nanopore runs. It can be used to produce general quality metrics from the per barcode FASTQ files generated by a basecaller e.g. quality score distribution, read lengths, and other general stats. You can also generate quality metrics per barcode.

![ToulligQC - Barcoding Report](images/toulligqc_barcoding_report.png)

## Alignment

<details markdown="1">
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113 changes: 19 additions & 94 deletions modules.json
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Expand Up @@ -7,167 +7,92 @@
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9 changes: 9 additions & 0 deletions modules/nf-core/toulligqc/environment.yml
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62 changes: 62 additions & 0 deletions modules/nf-core/toulligqc/main.nf
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66 changes: 66 additions & 0 deletions modules/nf-core/toulligqc/meta.yml
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -71,6 +71,7 @@ params {
// Options: QC
skip_qc = false
skip_nanoplot = false
skip_toulligqc = false
skip_fastqc = false
skip_multiqc = false

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