DIAMOND: only use READ1 for paired-end reads without merging #631
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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: 3.3.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Midnighter
previously requested changes
Aug 14, 2025
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I understand that you only changed the message, but are we sure that we want a warning message per sample? I can see pros and cons.
jfy133
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Aug 14, 2025
subworkflows/local/profiling.nf
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| log.warn("[nf-core/taxprofiler] DIAMOND does not accept paired-end files as input. To run DIAMOND on this sample, please merge reads (e.g. with --shortread_qc_mergepairs). Skipping DIAMOND for sample ${meta.id}.") | ||
| log.warn("[nf-core/taxprofiler] DIAMOND does not accept paired-end files as input. For this sample, please merge reads (e.g. with --shortread_qc_mergepairs --shortread_qc_includeunmerged) or only Read 1 will be used without merging. Running DIAMOND for sample ${meta.id} using only Read 1. ") | ||
| } | ||
| meta.single_end |
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Just a warning message for paired-reads. Should I completely remove this warning message and document it in the usage?
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no I meant the meta.single_end line 😬
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I've tested single_end reads and the output looks good.
sample,run_accession,instrument_platform,fastq_1,fastq_2,fasta
2611,ERR5766174,ILLUMINA,,,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fasta/ERX5474930_ERR5766174_1.fa.gz
2612,ERR5766180,ILLUMINA,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERX5474936_ERR5766180_1.fastq.gz,,
ERR3201952,ERR3201952,OXFORD_NANOPORE,https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/data/fastq/ERR3201952.fastq.gz,,
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Or what do you mean here?
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
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You could do, you could have a run mixing SE and PE data |
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@nf-core-bot fix linting |
jfy133
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Aug 19, 2025
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Couple minor things but it otherwise looks good to me - thanks @LilyAnderssonLee for the fast fix!
subworkflows/local/profiling.nf
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| log.warn("[nf-core/taxprofiler] DIAMOND does not accept paired-end files as input. To run DIAMOND on this sample, please merge reads (e.g. with --shortread_qc_mergepairs). Skipping DIAMOND for sample ${meta.id}.") | ||
| log.warn("[nf-core/taxprofiler] DIAMOND does not accept paired-end files as input. For this sample, please merge reads (e.g. with --shortread_qc_mergepairs --shortread_qc_includeunmerged) or only Read 1 will be used without merging. Running DIAMOND for sample ${meta.id} using only Read 1. ") | ||
| } | ||
| meta.single_end |
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no I meant the meta.single_end line 😬
Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
Midnighter
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Aug 19, 2025
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Clean work! I hope enough people look at the docs and/or pay attention to the warning 😉
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I've found a possible bug: I think it's badly parsing the input file when it's a single path and not a list, so it's taking 'worksppace' as the root folder. |
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I added some dumps (but you can also check work directories), that the following commands worked as expectd:
Could you please cross check @LilyAnderssonLee ? |
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I have tested and got the results as you described. |
| reads: [it[0] + it[2], it[1]] | ||
| db: [it[2], it[3]] | ||
| reads: [meta + meta_db, meta.single_end ? reads : reads[0]] | ||
| db: [meta_db, db] |
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@jfy133 I spotted the error. filter condition actually only allows single-end reads to proceed to DIAMOND analysis. I have tested this one and it should work now.
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Ooops yes good catch!
I think the change makes sense, as we no-longer have to distinguish between single nor paired end (we just take R1 from paired end), so no filtering necessary 👍
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@nf-core-bot fix linting |
jfy133
approved these changes
Aug 26, 2025
| reads: [it[0] + it[2], it[1]] | ||
| db: [it[2], it[3]] | ||
| reads: [meta + meta_db, meta.single_end ? reads : reads[0]] | ||
| db: [meta_db, db] |
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Ooops yes good catch!
I think the change makes sense, as we no-longer have to distinguish between single nor paired end (we just take R1 from paired end), so no filtering necessary 👍
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PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).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).