added seqfu stats #56
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
MatthiasZepper
requested changes
Oct 29, 2024
There was a problem hiding this comment.
Thank you for your contribution!
Ultimately, the pipeline will allow to flexibly choose the tools that are run, so having more tools in the pipeline is always great, but what exactly was your rationale here?
Admittedly, I just skimmed over the description, but to me, it seems that it is predominantly meant to run on FASTA files and for judging the quality of genome assemblies. Unless I missed some relevant arguments, its application on sequencing reads is in my opinion does not really yield too many meaningful statistics (at least for Illumina, for Nanopore probably yes)
Do you happen to have a Nanopore example? For Illumina, this is basically all you get:
┌──────────────────────────┬──────────┬────────────┬───────┬─────┬─────┬─────┬───────┬─────┬─────┐
│ File │ #Seq │ Total bp │ Avg │ N50 │ N75 │ N90 │ auN │ Min │ Max │
├──────────────────────────┼──────────┼────────────┼───────┼─────┼─────┼─────┼───────┼─────┼─────┤
│ S11_L001_R1_001.fastq.gz │ 35875355 │ 5417178605 │ 151.0 │ 151 │ 151 │ 151 │ 0.000 │ 151 │ 151 │
│ S11_L001_I1_001.fastq.gz │ 35875355 │ 322878195 │ 9.0 │ 9 │ 9 │ 9 │ 0.000 │ 9 │ 9 │
│ S11_L001_R2_001.fastq.gz │ 35875355 │ 5417178605 │ 151.0 │ 151 │ 151 │ 151 │ 0.000 │ 151 │ 151 │
└──────────────────────────┴──────────┴────────────┴───────┴─────┴─────┴─────┴───────┴─────┴─────┘
But with regard to the code, this already looks very good and tidy!
I am only missing a config for the module with a publishDir directive, so that the reports from the stats output channel are published in a subfolder of the outdir. Furthermore, there are possibly relevant ext.args that I overlooked and that you used for the reads?
Hi @MatthiasZepper, thank you for your comments! To be fair, I took up this issue/PR to "prepare" the pipeline with as many new modules as possible. I agree that this tool is more useful with Nanopore reads. Maybe this PR can be "frozen" until the seqinspector pipeline has a workflow for Nanopore/long read methods. Or until the pipeline accepts files that are not FASTQ (FASTA, BAM, BED, etc). Unfortunately, I don't have a Nanopore example, I'll see if there is some nanopore dataset on the test-datasets repo so I can see what the stats look like. I'll add now the config for the |
MatthiasZepper
approved these changes
Nov 5, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Added SeqFu stats module
PR checklist
nf-core lint).nf-test test main.nf.test -profile test,docker).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).