Feat dnascope #180
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Feat dnascope #180
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jemten
approved these changes
May 17, 2022
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Great work @ramprasadn and @sima-r. Some small questions but I think it looks good otherwise. Choose if you want to address them 😄
conf/genomes.config
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| @@ -28,11 +30,13 @@ params { | |||
| 'GRCh38' { | |||
| fasta = "${params.local_genomes}/grch38_homo_sapiens_-assembly-.fasta" | |||
| fai = "${params.local_genomes}/grch38_homo_sapiens_-assembly-.fasta.fai" | |||
| bwa = "${params.local_genomes}/bwa/" | |||
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Would be nice to have the same format on bwa and the bwamem2 index.
Could you do "${params.local_genomes}/grch38_homo_sapiens_-assembly-.fasta.{amb,ann,bwt,pac,sa}"?
| --algo DNAModelApply \\ | ||
| --model $ml_model \\ | ||
| -v $vcf \\ | ||
| ${prefix}_dnascope_ml.vcf |
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Is it possible to have this produce bgzipped output?
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It is possible; sentieon uses a separate module (util vcfconvert) for compression. However, that module doesn't accept input from terminal so using pipe is not an option, and so it has to be a separate step in the pipeline.
Also, I didn't focus so much on the compression here because vcf files generated here will have to be combined in the next step to generate a single multisample vcf in case of duos and trios. Since we will only publish that multisample vcf, it made sense to compress that file directly and not these individual sample vcfs. What do you think?
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Just adding .gz to file extension did the trick! 😄
modules/local/sentieon/dnascope.nf
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| $dbsnp \\ | ||
| $args2 \\ | ||
| $model \\ | ||
| ${prefix}_dnascope.vcf |
sima-r
approved these changes
May 17, 2022
| bwamem2 = "${params.local_genomes}/grch38_homo_sapiens_-assembly-.fasta.{0123,amb,ann,bwt.2bit.64,pac}" | ||
| call_interval = "" |
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You have call_interval variable here assuming this holding a bed file I guess? Would it be ok to have it here if one wants to give only some particular chromosomes?
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The problem here is that if I assume they are going to send in a value and they use a path(file), then the file won't get staged in the work directory. But if I assume then the input is going to be a file, I can create a path-type channel, which will stage the file in the work directory by default. And one can always put the chromosomes they are interested in, in a file. That's why I chose to do the latter.
modules/local/sentieon/dnascope.nf
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' |
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what happened to args3 which returned call_inretvals var? Maybe you wanted to leave it for sites' config?
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oh I see what was the change, never mind this comment! :D
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Actually, I realized having call_intervals in modules.config will not work if the user gives a file as an input so I have moved it back into the module..
jemten
reviewed
May 18, 2022
Co-authored-by: Anders Jemt <jemten@users.noreply.github.com>
This was referenced Aug 11, 2022
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PR checklist
This PR adds sentieon's dnamodelapply and dnascope modules, places them in a subworkflow, and makes relevant changes in other parts of the workflow.
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR> -stub).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).