create template GENERATE_DOWNSTREAM_SAMPLESHEETS for tools #3261
Conversation
Joon-Klaps
changed the title
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' |
There was a problem hiding this comment.
do we need to have that as a default?
There was a problem hiding this comment.
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.
There was a problem hiding this comment.
@jfy133 I like that idea. But we should be carefull not to make it to complex.
nf_core/pipeline-template/subworkflows/local/generate_downstream_samplesheets/main.nf
Outdated
Show resolved
Hide resolved
| 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] | ||
| } |
There was a problem hiding this comment.
are we sure we want it to make so genomics specific?
There was a problem hiding this comment.
See reply above about pros/cons of example code (maybe with more TODOs.
|
Pending fix here: nextflow-io/nextflow#5465 |
PR checklist
Solves #3259
CHANGELOG.mdis updateddocsis updated