Add support for generating mag samplesheet #544
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jfy133
reviewed
Oct 14, 2024
| } | ||
| .tap { ch_colnames } | ||
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| channelToSamplesheet(ch_colnames, ch_list_for_samplesheet, 'downstream_samplesheets', format, format_sep) |
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Joon has updated the function to also include the pipeline name as an additional argument, please check detaxier for the example (this will be helpful when @LilyAnderssonLee 's differentialabundance PR comes in :)
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| def short_reads_1 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_1.getName() | ||
| def short_reads_2 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_2.getName() |
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Can you not also make this support single_end using the meta.single_end information?
Or have we lost that information at this stage?
Suggested change
| def short_reads_1 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_1.getName() | |
| def short_reads_2 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_2.getName() | |
| def short_reads_1 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_1.getName() | |
| def short_reads_2 = !meta.single_end ? file(params.outdir).toString() + '/' + meta.id + '/' + fastq_2.getName() : "" |
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I do not follow here. We said to filter out the single ends and fasta. Or do I misunderstand something?
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Ah yeah, good point I forgot and there wasn't a comment why 😅
Please leave a comment next to the line saying only PE supported now, and I'll look into fixing that later :)
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@sofstam did you see what @Joon-Klaps did in detaxizer for SE/PE reads? You can copy the same concept here too (basically to branch SE/PE separately, and call the channelToSamplesheet function twice ;)
Co-authored-by: James A. Fellows Yates <[email protected]>
…profiler into generate-samplesheet
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@nf-core-bot fix linting |
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jfy133
reviewed
Oct 16, 2024
docs/output.md
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| <summary>Output files</summary> | ||
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| - `downstream_samplesheets/` | ||
| - `mag.csv`: input sheet for nf-core/mag with paths to nf-core/taxprofiler preprocessed (corresponding to what is saved with `--save_analysis_ready_fastqs`) |
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Missing differential abundance? @LilyAnderssonLee do you thin kyou could merge your PR into this one at this stage?
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| def short_reads_1 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_1.getName() | ||
| def short_reads_2 = file(params.outdir).toString() + '/' + meta.id + '/' + fastq_2.getName() |
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@sofstam did you see what @Joon-Klaps did in detaxizer for SE/PE reads? You can copy the same concept here too (basically to branch SE/PE separately, and call the channelToSamplesheet function twice ;)
subworkflows/local/generate_downstream_samplesheets/tests/main.nf.test
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Co-authored-by: James A. Fellows Yates <[email protected]>
Co-authored-by: James A. Fellows Yates <[email protected]>
…profiler into generate-samplesheet
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@nf-core-bot fix linting |
jfy133
reviewed
Oct 24, 2024
sofstam
commented
Oct 24, 2024
docs/output.md
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| @@ -758,7 +758,9 @@ The pipeline can also generate input files for the following downstream pipeline | |||
| <summary>Output files</summary> | |||
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| - `downstream_samplesheets/` | |||
| - `mag.csv`: input sheet for that contains paths to preprocessed FASTQs (corresponding to what is saved with `--save_analysis_ready_fastqs`) that can be used to skip read preprocessing steps in nf-core/mag | |||
| - `mag-{pe,se}.csv`: input sheet for single-end and paired-end reads that contains paths to preprocessed short-read FASTQs (corresponding to what is saved with `--save_analysis_ready_fastqs`) that can be used to skip read preprocessing steps in nf-core/mag. | |||
| - Note: if you merge reads, these will be listed in teh `mag-se.csv`. | |||
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Cannot make a suggestion but:
teh mag-se.csv. -> the mag-se.csv.
| pe: true | ||
| } | ||
| pe: it.short_reads_2 != "" | ||
| unknown: true |
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Why is the unknown: true here?
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I think we are almost there, for some reason we get extra files in |
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Closes #542
PR checklist
nf-core 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).