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create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools #3261

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PR checklist

Solves #3259

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

@Joon-Klaps Joon-Klaps changed the title init create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools Oct 29, 2024
This commit refactors the generate_downstream_samplesheets subworkflow in the pipeline-template. It updates the workflow to a specific pipeline and adds support for more pipelines in the future. The changes include modifying the input parameters and updating the channelToSamplesheet function. This refactoring improves the flexibility and extensibility of the subworkflow.
{% if downstream_samplesheets -%}
// Downstream samplesheets
generate_downstream_samplesheets = true
generate_pipeline_samplesheets = 'rnaseq'
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do we need to have that as a default?

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It think we need to add more TODO statemetns next to this, I'm in two minds whether we should put an example or empty.

The whole thing might not be immediately obvious how to adapt without the example. For example I would actually extend the example to comma separated list as this is supported.

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@jfy133 I like that idea. But we should be carefull not to make it to complex.

CHANGELOG.md Outdated Show resolved Hide resolved
Comment on lines 18 to 25
ch_list_for_samplesheet = ch_reads.map { meta, reads ->
def out_path = file(params.outdir).toString() + '/relative/custom/path/'
def sample = meta.id
def fastq_1 = meta.single_end ? out_path + reads.getName() : out_path + reads[0].getName()
def fastq_2 = !meta.single_end ? out_path + reads[1].getName() : ""
def strandedness = "auto"
[sample: sample, fastq_1: fastq_1, fastq_2: fastq_2, strandedness: strandedness]
}
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are we sure we want it to make so genomics specific?

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See reply above about pros/cons of example code (maybe with more TODOs.

nf_core/pipelines/create/template_features.yml Outdated Show resolved Hide resolved
nf_core/pipelines/create/template_features.yml Outdated Show resolved Hide resolved
@ewels ewels added this to the 3.2 milestone Nov 21, 2024
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jfy133 commented Nov 21, 2024

Pending fix here: nextflow-io/nextflow#5465

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5 participants