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feat: Delly automated conversion of output file (#468)
* Allowed for any output format * Automated conversion of output file * Updated wrapper-utils
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Original file line number | Diff line number | Diff line change |
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@@ -1,4 +1,15 @@ | ||
name: delly | ||
description: Call variants with delly. | ||
url: https://github.com/dellytools/delly | ||
authors: | ||
- Johannes Köster | ||
- Filipe G. Vieira | ||
input: | ||
- BAM/CRAM file(s) | ||
- reference genome | ||
- BED file (optional) | ||
output: | ||
- VCF/BCF with SVs. | ||
notes: | | ||
* The `uncompressed_bcf` param sets output to uncompressed BCF (ignored if output is `vcf` or `vcf.gz`) | ||
* The `extra` param allows for additional program arguments |
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Original file line number | Diff line number | Diff line change |
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@@ -1,15 +1,33 @@ | ||
rule delly: | ||
rule delly_bcf: | ||
input: | ||
ref="genome.fasta", | ||
samples=["mapped/a.bam"], | ||
# optional exclude template (see https://github.com/dellytools/delly) | ||
exclude="human.hg19.excl.tsv" | ||
alns=["mapped/a.bam"], | ||
# optional | ||
exclude="human.hg19.excl.tsv", | ||
output: | ||
"sv/calls.bcf" | ||
"sv/calls.bcf", | ||
params: | ||
extra="" # optional parameters for delly (except -g, -x) | ||
uncompressed_bcf=True, | ||
extra="", # optional parameters for delly (except -g, -x) | ||
log: | ||
"logs/delly.log" | ||
"logs/delly.log", | ||
threads: 2 # It is best to use as many threads as samples | ||
wrapper: | ||
"master/bio/delly" | ||
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rule delly_vcfgz: | ||
input: | ||
ref="genome.fasta", | ||
alns=["mapped/a.bam"], | ||
# optional | ||
exclude="human.hg19.excl.tsv", | ||
output: | ||
"sv/calls.vcf.gz", | ||
params: | ||
extra="", # optional parameters for delly (except -g, -x) | ||
log: | ||
"logs/delly.log", | ||
threads: 2 # It is best to use as many threads as samples | ||
wrapper: | ||
"master/bio/delly" |
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