CI
1ebb61f1e8
Build pipeline: vsh-ci-dev-jsbwk
Source commit: 1e1ffb315f
Source message: Merge pull request #17 from viash-hub/add_biobox_modules
- Migrate a number of components to biobox
- Fix tests
- Reduce size of test resources
- Prepare for Viash Hub
50 lines
2.7 KiB
Bash
Executable File
50 lines
2.7 KiB
Bash
Executable File
#!/bin/bash
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CURR=`pwd`
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DEST="testData/unit_test_resources"
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mkdir -p $DEST
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cd $DEST
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echo "Fetching unit test resources..."
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## UMI_TOOLS
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# extract
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wget https://github.com/CGATOxford/UMI-tools/raw/master/tests/slim.fastq.gz
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wget https://github.com/CGATOxford/UMI-tools/raw/master/tests/scrb_seq_fastq.1.gz
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wget https://github.com/CGATOxford/UMI-tools/raw/master/tests/scrb_seq_fastq.2.gz
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# dedup
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wget https://github.com/CGATOxford/UMI-tools/raw/master/tests/chr19.bam
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wget https://github.com/CGATOxford/UMI-tools/raw/master/tests/chr19.bam.bai
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# MultiQC
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wget https://multiqc.info/examples/rna-seq/data.zip
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# dupRadar
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wget https://github.com/ssayols/dupRadar/raw/master/inst/extdata/genes.gtf
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wget https://github.com/ssayols/dupRadar/raw/master/inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam
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wget https://github.com/ssayols/dupRadar/raw/master/inst/extdata/wgEncodeCaltechRnaSeqGm12878R1x75dAlignsRep2V2.bam.bai
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### Resources from https://github.com/snakemake/snakemake-wrappers/tree/master/bio
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# DESeq2
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wget https://github.com/snakemake/snakemake-wrappers/raw/master/bio/deseq2/deseqdataset/test/dataset/counts.tsv
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# preseq lc_extrap
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wget https://github.com/snakemake/snakemake-wrappers/raw/master/bio/preseq/lc_extrap/test/samples/a.sorted.bed
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wget https://github.com/smithlabcode/preseq/raw/master/data/SRR1106616_5M_subset.bam
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### nf-core test datasets
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# sarscov2
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mkdir -p sarscov2
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wget -O sarscov2/genome.sizes https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.sizes
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wget -O sarscov2/test.bedgraph https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/illumina/bedgraph/test.bedgraph
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wget -O sarscov2/genome.fasta https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta
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wget -O sarscov2/genome.fasta.fai https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta.fai
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wget -O sarscov2/test.paired_end.sorted.bam https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam
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wget -O sarscov2/test.paired_end.sorted.bam.bai https://github.com/nf-core/test-datasets/raw/modules/data/genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai
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wget -O sarscov2/test.bed https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/bed/test.bed
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wget -O sarscov2/test.bed12 https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/bed/test.bed12
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wget -O sarscov2/genome.gtf https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.gtf
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cd $CURR |