Add a task for SnpSift filter and update snpEff#340
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…en run on dnanexus
rhpvorderman
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rhpvorderman
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Looks good to me. I did found some nitpicks.
bcftools.wdl
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| String? regions | ||
| Boolean splitMultiallelicSites = false | ||
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| String memory = "64GiB" |
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That seems quite a lot. Does it read everything into memory?
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Yeah, it doesn't need that much, but I needed dnanexus to select a larger VM type with enough scratch space to fit the output file in. I couldn't find a way to do that differently :/ I'll have another look, there should be a better way...
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There are disk space requirements in WDL I believe. We never used them because disk space is not exactly a problem on our storage. Or is that something for later versions?
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That was added in version 1.1, I believe. I did find an example in the dxcompiler docs using the disks runtime attribute, so I've just copied that now.
| mkdir -p "$(dirname ~{outputPath})" | ||
| bcftools norm \ | ||
| -o ~{outputPath} \ | ||
| -O ~{true="z" false="v" compressed} \ |
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There is an opportunity here to set it by default to z1:
-O, --output-type u|b|v|z[0-9] u/b: un/compressed BCF, v/z: un/compressed VCF, 0-9: compression level [v]
That way it is always quite fast.
snpsift.wdl
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| command { | ||
| set -e | ||
| ls ~{vcf} ~{vcfIndex} |
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Seems like an old debug command got in the task.
snpeff.wdl
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| command { | ||
| set -e | ||
| ls ~{vcf} ~{vcfIndex} |
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Is this a debug command?
bcftools.wdl
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| command { | ||
| set -e | ||
| ls ~{inputFile} ~{inputFileIndex} |
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Is this a debug command?
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No, this is a workaround for dxcompiler. It will only localize files mentioned in the command.
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Oh, fun, galaxy has the same issue with pulsar.
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🤦♂️ . There is probably a reason for this design decision? Or is it an oversight? Should we file a bug?
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There's an issue open for in on their repo, but they claimed that: "WDL spec did not specify (it specifies the WDL syntax rather than the execution environment behavior)". Which is simply not true...
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Checklist
parameter_metawas added/updated (if required).