├── .gitignore ├── CONTRIBUTING_NextFlow.md ├── LICENSE ├── README.md ├── config ├── gcp.nf.conf └── local.nf.conf ├── example_inputs ├── test.fq2bam.json └── test.germline.json ├── nextflow ├── bwa_deepvariant.nf ├── fq2bam.nf └── germline.nf └── test ├── .nextflow.log.1 ├── .nextflow.log.2 ├── .nextflow.log.3 ├── .nextflow.log.4 └── fq2bam.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/.gitignore -------------------------------------------------------------------------------- /CONTRIBUTING_NextFlow.md: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/README.md -------------------------------------------------------------------------------- /config/gcp.nf.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/config/gcp.nf.conf -------------------------------------------------------------------------------- /config/local.nf.conf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/config/local.nf.conf -------------------------------------------------------------------------------- /example_inputs/test.fq2bam.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/example_inputs/test.fq2bam.json -------------------------------------------------------------------------------- /example_inputs/test.germline.json: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/example_inputs/test.germline.json -------------------------------------------------------------------------------- /nextflow/bwa_deepvariant.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/nextflow/bwa_deepvariant.nf -------------------------------------------------------------------------------- /nextflow/fq2bam.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/nextflow/fq2bam.nf -------------------------------------------------------------------------------- /nextflow/germline.nf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/nextflow/germline.nf -------------------------------------------------------------------------------- /test/.nextflow.log.1: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/test/.nextflow.log.1 -------------------------------------------------------------------------------- /test/.nextflow.log.2: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/test/.nextflow.log.2 -------------------------------------------------------------------------------- /test/.nextflow.log.3: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/test/.nextflow.log.3 -------------------------------------------------------------------------------- /test/.nextflow.log.4: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/test/.nextflow.log.4 -------------------------------------------------------------------------------- /test/fq2bam.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/clara-parabricks-workflows/parabricks-nextflow/HEAD/test/fq2bam.sh --------------------------------------------------------------------------------