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fix: log file handling and other small improvements for bcftools wrap…
…pers (#429) * Added logs to several bcftools modules * Added bcftools_opts to norm * Added snakemake-wrapper-utils * Added params extra, to be consistent with other modules * Disabled parsing of memory and temp_dir * Formatting with snakefmt * Added test * Fixed typo * Added missing extra param
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Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -2,4 +2,5 @@ channels: | |
- bioconda | ||
- conda-forge | ||
dependencies: | ||
- bcftools =1.11 | ||
- bcftools =1.11 | ||
- snakemake-wrapper-utils =0.2 |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,9 +1,11 @@ | ||
rule norm_vcf: | ||
input: | ||
"{prefix}.vcf" | ||
"{prefix}.bcf", | ||
output: | ||
"{prefix}.vcf" | ||
"{prefix}.norm.vcf", | ||
log: | ||
"{prefix}.norm.log", | ||
params: | ||
"" # optional parameters for bcftools norm (except -o) | ||
extra="--rm-dup none", # optional | ||
wrapper: | ||
"master/bio/bcftools/norm" |
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