Simplify hello-gatk #364
Simplify hello-gatk #364
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… methods. This should make it quicker and cleaner to use as training material.
… more approachable methods.
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| params.reads_bam = "./data/samplesheet.csv" | ||
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| // Accessory files | ||
| params.genome_reference = "${projectDir}/data/ref/ref.fasta" | ||
| params.genome_reference_index = "${projectDir}/data/ref/ref.fasta.fai" | ||
| params.genome_reference_dict = "${projectDir}/data/ref/ref.dict" | ||
| params.calling_intervals = "${projectDir}/data/intervals.list" | ||
| params.reference = "./data/ref/ref.fasta" | ||
| params.reference_index = "./data/ref/ref.fasta.fai" | ||
| params.reference_dict = "./data/ref/ref.dict" | ||
| params.calling_intervals = "./data/intervals.list" |
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workflow.projectDir doesn't exist in the configuration, so we just use a relative path.
We could wrap it in closures but that makes it complicated.
Co-authored-by: Marcel Ribeiro-Dantas <[email protected]>
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A small side benefit I noticed while testing, because the two containers share most of the layers downloading them is much more efficient. |
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Reviewing the overall flow right now, at first and second glance everything looks really good, I like that this is simpler. We can always demonstrate more advanced stuff in later trainings. One quick comment is I noticed the new use of Also I noticed this numbering/header issue: 
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@adamrtalbot Just a heads up that we'd like to merge this for our training in SF tomorrow. |
I'm happy with it, if you are hit merge. Currently needs an approval 😉 |
I've reviewed in more detail and I feel like there's a couple of things that are a bit of a jump, so I'm making an intermediate version with most but not all of the changes |
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I've just tried removing the reference channels and it still works. From: to: So let's do that. In addition, we should remove |
Based on Adam's branch at #364
* Simplified version of Hello-GATK Based on Adam's branch at #364 * Intermediate scripts by section * starter script for hello-gatk * Replace bams with Adam's * Add Adam's smaller reference files * Delete hello-nextflow/data/samplesheet.csv No longer needed * Delete hello-nextflow/data/ref.tar.gz replaced by Adam's ref files * Delete hello-nextflow/data/intervals.list reolaced by Adam's BED file * Move ref under data (oops) * convert fromPath().collect() to file() For accessory file inputs * Prettier fixes whitespace * addressing review - add note about working directory - remove collect mention which is no longer applicable and replace with informative statement
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Most of the changes in here were made in my recent PR (thanks @adamrtalbot for your hard work!) so this is no longer going to be used, but I'm leaving it open for now in case there's anything else we want to pilfer from it. |
This PR simplifies the hello-gatk example.
collect), which makes it more obvious what each step doesNegatives:
chr20:coordinateStart-coordinateEnd) which is harder to develop for usResolves #355