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Seqkit #59

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Seqkit #59

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dad5d6d
add seqkit module
sarahjeeeze Oct 28, 2024
d806380
seqkit
sarahjeeeze Oct 29, 2024
48ccc66
update docs
sarahjeeeze Oct 29, 2024
879b579
docs
sarahjeeeze Oct 29, 2024
1f582fe
fix-ci
sarahjeeeze Oct 29, 2024
de4bee8
actually add the module
sarahjeeeze Oct 29, 2024
9cd232c
changelog
sarahjeeeze Oct 29, 2024
eeb1577
update docs
sarahjeeeze Oct 30, 2024
60cb044
mangled
sarahjeeeze Oct 30, 2024
f802608
fix gnarly spacing
sarahjeeeze Oct 30, 2024
76b882d
unmangle modules.json
sarahjeeeze Oct 30, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#20](https://github.com/nf-core/seqinspector/pull/20) Use tags to generate group reports
- [#13](https://github.com/nf-core/seqinspector/pull/13) Generate reports per run, per project and per lane.
- [#49](https://github.com/nf-core/seqinspector/pull/49) Merge with template 3.0.2.
- [#40](https://github.com/nf-core/seqinspector/pull/59) Seqkit Stats TSV output.
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### `Fixed`

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4 changes: 4 additions & 0 deletions CITATIONS.md
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Expand Up @@ -18,6 +18,10 @@

> Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.

- [Seqkit](https://doi.org/10.1371/journal.pone.0163962)

> Shen W, Le S, Li Y, Hu F (2016) SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation. PLoS ONE 11(10): e0163962.

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## Software packaging/containerisation tools

- [Anaconda](https://anaconda.com)
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -33,6 +33,7 @@

1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))
2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))
3. Provide Seqkit summary stats ([`SeqkitStats`](https://bioinf.shenwei.me/seqkit/usage/#stats))

## Usage

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4 changes: 4 additions & 0 deletions conf/modules.config
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Expand Up @@ -22,6 +22,10 @@ process {
ext.args = '--quiet'
}

withName: SEQKIT_STATS {
ext.args = ''
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Don't you not want to publish the results as well in the outdir? Or only MultiQC?

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yeah it is defined here - I guess you would only overwrite it if you dont want your output published in the standard way.

seqinspector/conf/modules.config

Line 15 in 9cd232c

publishDir = [

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Oooh fancy - a central publishDir directive for all modules ?!? That's smart and has totally escaped me...sorry then for the false accusations!

}

withName: 'MULTIQC_GLOBAL' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
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13 changes: 13 additions & 0 deletions docs/output.md
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Expand Up @@ -12,6 +12,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d

- [FastQC](#fastqc) - Raw read QC
- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline
- [SeqkitStats](#seqkitstats) - Per sample TSV file with summary statistics
- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution

### FastQC
Expand Down Expand Up @@ -59,6 +60,18 @@ nf-core/seqinspector will generate the following MultiQC reports:

Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see <http://multiqc.info>.

### SeqkitStats

<details markdown="1">
<summary>Output files</summary>

- `seqkit/`
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- `*.tsv`: Per sample TSV file with summary statistics.

</details>

[SeqkitStats](https://bioinf.shenwei.me/seqkit/usage/#stats) it gives general quality metrics about your sequenced reads including average read lengths, GC(%) and n50's. For further reading and documentation see the [Seqkit help pages]([Seqkit help](https://bioinf.shenwei.me/seqkit/)).
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It is true that SeqkitStats computes some quality metrics, but to my best knowledge it is more useful for FASTA files and genomic assemblies than sequencing reads?

For example, for an Illumina run, an average read length prior to trimming should be known, because it corresponds to the number of cycles. For Nanopore, admittedly, such a statistic is more useful, so you may want to structure the documentation accordingly?

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@sarahjeeeze sarahjeeeze Oct 30, 2024 •
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Updated text a little, should i specifically mention this is more useful for nanopore data? for ilumina etc you do still get n50's etc but agree it is less useful - want me to add a nanopore test? :D

file	format	type	num_seqs	sum_len	min_len	avg_len	max_len	Q1	Q2	Q3	sum_gap	N50	N50_num	Q20(%)	Q30(%)	AvgQual	GC(%)
sample1_R1.fastq.gz	FASTQ	DNA	1377513	411872902	35	299.0	301	300.0	301.0	301.0	0	301	1	99.10	97.54	29.31	38.53
sample1_R2.fastq.gz	FASTQ	DNA	1377513	411840994	35	299.0	301	300.0	301.0	301.0	0	301	1	97.11	93.54	25.78	38.54


### Pipeline information

<details markdown="1">
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5 changes: 5 additions & 0 deletions modules.json
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Expand Up @@ -14,6 +14,11 @@
"branch": "master",
"git_sha": "cf17ca47590cc578dfb47db1c2a44ef86f89976d",
"installed_by": ["modules"]
},
"seqkit/stats": {
"branch": "master",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
}
}
},
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5 changes: 5 additions & 0 deletions modules/nf-core/seqkit/stats/environment.yml
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34 changes: 34 additions & 0 deletions modules/nf-core/seqkit/stats/main.nf
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48 changes: 48 additions & 0 deletions modules/nf-core/seqkit/stats/meta.yml
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141 changes: 141 additions & 0 deletions modules/nf-core/seqkit/stats/tests/main.nf.test
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