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Workflow outputs (second preview) #30
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Signed-off-by: Ben Sherman <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Dr Marco Claudio De La Pierre <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
…f into workflow-output-dsl Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
Signed-off-by: Ben Sherman <[email protected]>
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output { | ||
samples { | ||
path { id, _quant, _fastqc -> "${workflow.outputDir}/${id}" } |
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this is a bug in the workflow output DSL, it is not resolving the dynamic name against the base output directory
samples_ch = RNASEQ.out.quant | ||
| join(RNASEQ.out.fastqc) |
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this change is the important bit -- we are joining the metadata, fastqc logs, and quant results for each sample into a single channel, and publishing that channel
then the path
target directive is used to control the output directory structure
Signed-off-by: Ben Sherman <[email protected]>
The output directory looks like this: $ find results/ | sort
results/
results/ggal_gut
results/ggal_gut/fastqc
results/ggal_gut/quant
results/index.json
results/multiqc_report.html And the index file looks like this: [
{
"id": "ggal_gut",
"quant": "/home/bent/projects/nextflow-io_rnaseq-nf/results/quant",
"fastqc": "/home/bent/projects/nextflow-io_rnaseq-nf/results/fastqc"
}
] |
Second iteration based on #27
This PR takes a different approach to workflow outputs by defining a
samples
target instead of having a target for each tool. The difference is harder to see here since we only publish the fastqc logs for each sample, but it is more clear for nf-core pipelines like fetchngs and rnaseq.I originally treated each tool as an output target, but then I realized that it makes more sense to have a single output target that joins all results pertaining to a sample. This makes it much easier for a downstream pipeline to consume the outputs, because now instead of joining multiple index files, a downstream pipeline need only take a subset from the one index file.
It also publishes the salmon output, which is not essential, but demonstrates the idea of a "sample" being all results associated with a particular sample id.
The
multiqc
target could also be calledsummary
, to denote that it contains the all of the summary results.