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Simplified version of Hello-GATK (#376)
* Simplified version of Hello-GATK Based on Adam's branch at #364 * Intermediate scripts by section * starter script for hello-gatk * Replace bams with Adam's * Add Adam's smaller reference files * Delete hello-nextflow/data/samplesheet.csv No longer needed * Delete hello-nextflow/data/ref.tar.gz replaced by Adam's ref files * Delete hello-nextflow/data/intervals.list reolaced by Adam's BED file * Move ref under data (oops) * convert fromPath().collect() to file() For accessory file inputs * Prettier fixes whitespace * addressing review - add note about working directory - remove collect mention which is no longer applicable and replace with informative statement
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‎docs/hello_nextflow/03_hello_gatk.md‎

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‎hello-nextflow/data/bam/reads_father.bam‎

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‎hello-nextflow/data/bam/reads_mother.bam‎

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‎hello-nextflow/data/bam/reads_son.bam‎

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‎hello-nextflow/data/intervals.list‎

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‎hello-nextflow/data/ref.tar.gz‎

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‎hello-nextflow/data/ref/intervals.bed‎

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‎hello-nextflow/data/ref/ref.dict‎

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@HD VN:1.6
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@SQ SN:20_10037292_10066351 LN:29059 M5:d9a7bb8816cea7d1e5c55e00d1faeeb4 UR:reads_father_20_10037292_10066351.region.fasta

‎hello-nextflow/data/ref/ref.fasta‎

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‎hello-nextflow/data/ref/ref.fasta.fai‎

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