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MatthiasZepper
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Oct 29, 2024
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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 format type num_seqs sum_len min_len avg_len max_len
S11_L001_R1_001.fastq.gz FASTQ DNA 35875355 5417178605 151 151.0 151
S11_L001_R1_001.fastq.gz FASTQ DNA 35875355 322878195 9 9.0 9
S11_L001_R2_001.fastq.gz FASTQ DNA 35875355 5417178605 151 151.0 151
But with regard to the code, this already looks very good and tidy!
I am only missing a publishDir directive in the config, so that the reports from the stats output channel are published in a subfolder of the outdir.
MatthiasZepper
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Oct 30, 2024
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.0.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
MatthiasZepper
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Jun 12, 2026
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Looks good to me. A few minor remarks, but ultimately it is a question for the user which tools they want to run,
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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).