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fix: create tabix index sub-wrapper (#501)
* Created index sub-wrapper * Fixed tests, paths, updated version, and added extra info Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
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@@ -3,4 +3,4 @@ channels: | |
- bioconda | ||
- nodefaults | ||
dependencies: | ||
- htslib ==1.10 | ||
- htslib =1.15 |
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name: tabix | ||
description: Process given file with tabix (e.g., create index). | ||
url: https://www.htslib.org/doc/tabix.html#INDEXING_OPTIONS | ||
authors: | ||
- Johannes Köster | ||
input: | ||
- Bgzip compressed file (e.g. BED.gz, GFF.gz, or VCF.gz) | ||
output: | ||
- Tabix index file | ||
notes: | | ||
* Specify tabix index params (e.g. `-p vcf`) through `params`. |
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rule tabix: | ||
input: | ||
"{prefix}.vcf.gz", | ||
output: | ||
"{prefix}.vcf.gz.tbi", | ||
log: | ||
"logs/tabix/{prefix}.log", | ||
params: | ||
# pass arguments to tabix (e.g. index a vcf) | ||
"-p vcf", | ||
wrapper: | ||
"master/bio/tabix/index" |
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@@ -3,4 +3,4 @@ channels: | |
- bioconda | ||
- nodefaults | ||
dependencies: | ||
- htslib==1.12 | ||
- htslib =1.15 |
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name: tabix | ||
description: Query given file with tabix. | ||
url: https://github.com/samtools/htslib | ||
url: https://www.htslib.org/doc/tabix.html#QUERYING_AND_OTHER_OPTIONS | ||
authors: | ||
- William Rowell | ||
input: | ||
- Bgzip compressed file (e.g. BED.gz, GFF.gz, or VCF.gz) | ||
- Tabix index file | ||
- Region of interest to retrieve (params.region) | ||
output: | ||
- Uncompressed subset of the input file from the given region | ||
notes: | | ||
* The `region` param (required) allows to specify region of interest to retrieve. | ||
* The `extra` param allows for additional program arguments. |
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rule tabix: | ||
input: | ||
"{prefix}.bed.gz", | ||
"{prefix}.bed.gz.tbi" | ||
## list the VCF/BCF as the first input | ||
## and the index as the second input | ||
"{prefix}.bed.gz", | ||
"{prefix}.bed.gz.tbi", | ||
output: | ||
"{prefix}.output.bed" | ||
params: | ||
region = "1" | ||
"{prefix}.output.bed", | ||
log: | ||
"logs/tabix/query/{prefix}.log" | ||
"logs/tabix/query/{prefix}.log", | ||
params: | ||
region="1", | ||
extra="", | ||
wrapper: | ||
"master/bio/tabix/query" |
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