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README.md
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| The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). | The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). | ||||
| ### New Releases | ### New Releases | ||||
| * The TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. | |||||
| * TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. | |||||
| * The `corealigner` step has been removed. | * The `corealigner` step has been removed. | ||||
| * The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`. | * The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`. | ||||
| * Some parameters' details have been changed, such as the `interval_list` has turned into `interval`. | |||||
| ### Getting Started | ### Getting Started | ||||
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tasks/Realigner.wdl
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| nt=$(nproc) | nt=$(nproc) | ||||
| if [ ${regions} ]; then | if [ ${regions} ]; then | ||||
| INTERVAL="--interval_list ${regions}" | |||||
| INTERVAL="--interval ${regions}" | |||||
| else | else | ||||
| INTERVAL="" | INTERVAL="" | ||||
| fi | fi |
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