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| path "${design.baseName}_design.tsv", emit: ch_expdesign | ||
| path "${design.baseName}_config.tsv", emit: ch_config | ||
| path "${design.baseName}_openms_design.tsv", emit: ch_expdesign | ||
| path "${design.baseName}_openms_config.tsv", emit: ch_config |
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Why, the dataset needs to keep the design.baseName in ${design.baseName}_openms_config.tsv and ${design.baseName}_openms_design.tsv should we removed @jpfeuffer @daichengxin ? leave it something like:
- openms_design.tsv
- openms_config.tsv
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If you have multiple runs, you will never know which is which. Definitely keep the original name there.
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I would not call the config "openms config". The config is only for nextflow to fill the meta channel.
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If you have multiple runs, you will never know which is which. Definitely keep the original name there.
We have for the other files now no run_name for example for the msstats, for the triqler etc.
In the pipeline we don't allow running multiple experimental design, only one. Then the analysis always correspond to one.
For conssistency if we move to the appraoch ${design.baseName} whe should do it for all the outputs msstats, triqler, openms design, pmultiqc, etc.
jpfeuffer
reviewed
Jun 23, 2022
modules/local/pmultiqc/main.nf
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def disable_pmultqic = params.enable_pmultiqc ? "" : "--disable_plugin" | ||
| def disable_pmultqic = (params.enable_pmultiqc) && (params.export_mztab) ? "" : "--disable_plugin" |
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Spelling! disable_pmultiqc
jpfeuffer
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Jun 23, 2022
Co-authored-by: Julianus Pfeuffer <pfeuffer@informatik.uni-tuebingen.de>
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@daichengxin can you changed to:
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ypriverol
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jpfeuffer and
ypriverol
and removed request for
jpfeuffer
ypriverol
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Jun 24, 2022
| path "${design.baseName}_design.tsv", emit: ch_expdesign | ||
| path "${design.baseName}_config.tsv", emit: ch_config | ||
| path "${design.baseName}_openms_design.tsv", emit: ch_expdesign | ||
| path "${design.baseName}_openms_config.tsv", emit: ch_config |
Member
There was a problem hiding this comment.
If you have multiple runs, you will never know which is which. Definitely keep the original name there.
We have for the other files now no run_name for example for the msstats, for the triqler etc.
In the pipeline we don't allow running multiple experimental design, only one. Then the analysis always correspond to one.
For conssistency if we move to the appraoch ${design.baseName} whe should do it for all the outputs msstats, triqler, openms design, pmultiqc, etc.
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PR checklist
nf-core lint).nextflow run . -profile 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).