CI
4caaaf68ef
Build pipeline: openpipelines-bio.openpipeline.v4.0.0-kd9qj
Source commit: de02293c9e
Source message: Bump version to v4.0.0
42 lines
1.2 KiB
Bash
Executable File
42 lines
1.2 KiB
Bash
Executable File
#!/bin/bash
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set -eo pipefail
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# settings
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ID=demuxafy_test_data
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OUT=resources_test/$ID
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DIR="$OUT"
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mkdir -p "$OUT"
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cd "$OUT"
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# download demuxafy test dataset
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wget https://www.dropbox.com/s/m8u61jn4i1mcktp/TestData4PipelineSmall.tar.gz
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tar -xf TestData4PipelineSmall.tar.gz
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# bam and vcf file
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cp TestData4PipelineSmall/test_dataset.vcf .
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# extract chr from vcf file
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grep -w '^#\|^#CHROM\|^[1-2]' test_dataset.vcf > test_dataset_chr1_2.vcf
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grep -w '^#\|^#CHROM\|^[3-4]' test_dataset.vcf > test_dataset_chr3_4.vcf
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# barcode list
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cp TestData4PipelineSmall/test_dataset/outs/filtered_gene_bc_matrices/Homo_sapiens_GRCh38p10/barcodes.tsv .
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# subsetted bam and bai for souporcell
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wget https://www.dropbox.com/s/7ew5lt0msf4z5gj/chr_1_pooled.sorted.bam
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wget https://www.dropbox.com/s/tpplbj9sab9b2p4/chr_1_pooled.sorted.bam.bai
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# variants from mixed sample
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wget https://www.dropbox.com/s/btir7ge4kzc7tu1/mixed_variant.vcf
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# dsc_pileup output
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wget https://www.dropbox.com/s/17hj9i0yavtezx1/dsc_pileup.zip
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unzip dsc_pileup.zip
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# subsetted human genome reference
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wget https://www.dropbox.com/s/ynlce3g7nwxthwg/genome_chr1.fa
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# remove unnecessary files
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rm -rf TestData4PipelineSmall
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rm TestData4PipelineSmall.tar.gz
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rm dsc_pileup.zip |