CI
7645430e58
Build pipeline: viash-hub.biobox.v0.1-8mh8l
Source commit: b84b29747d
Source message: Bump version to v0.1.0
49 lines
1.9 KiB
Bash
49 lines
1.9 KiB
Bash
#!/bin/bash
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set -e
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## VIASH START
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## VIASH END
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#########################################################################################
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echo "> Prepare test data"
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cat > genome.fasta <<'EOF'
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>chr1
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TGGCATGAGCCAACGAACGCTGCCTCATAAGCCTCACACATCCGCGCCTATGTTGTGACTCTCTGTGAGCGTTCGTGGG
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GCTCGTCACCACTATGGTTGGCCGGTTAGTAGTGTGACTCCTGGTTTTCTGGAGCTTCTTTAAACCGTAGTCCAGTCAA
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TGCGAATGGCACTTCACGACGGACTGTCCTTAGCTCAGGGGA
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EOF
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cat > genes.gtf <<'EOF'
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chr1 example_source gene 0 50 . + . gene_id "gene1"; transcript_id "transcript1";
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chr1 example_source exon 20 40 . + . gene_id "gene1"; transcript_id "transcript1";
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EOF
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#########################################################################################
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echo "> Generate index"
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"$meta_executable" \
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${meta_cpus:+---cpus $meta_cpus} \
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--index "star_index/" \
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--genomeFastaFiles "genome.fasta" \
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--sjdbGTFfile "genes.gtf" \
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--genomeSAindexNbases 2
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files=("Genome" "Log.out" "SA" "SAindex" "chrLength.txt" "chrName.txt" "chrNameLength.txt" "chrStart.txt" "exonGeTrInfo.tab" "exonInfo.tab" "geneInfo.tab" "genomeParameters.txt" "sjdbInfo.txt" "sjdbList.fromGTF.out.tab" "sjdbList.out.tab" "transcriptInfo.tab")
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echo ">> Check if output exists"
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[ ! -d "star_index" ] && echo "Directory 'star_index' does not exist!" && exit 1
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for file in "${files[@]}"; do
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[ ! -f "star_index/$file" ] && echo "File '$file' does not exist in 'star_index'." && exit 1
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done
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echo ">> Check contents of output files"
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grep -q "200" "star_index/chrLength.txt" || (echo "Chromosome length in file 'chrLength.txt' is incorrect! " && exit 1)
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grep -q "chr1" "star_index/chrName.txt" || (echo "Chromosome name in file 'chrName.txt' is incorrect! " && exit 1)
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grep -q "chr1 200" "star_index/chrNameLength.txt" || (echo "Chromosome name in file 'chrNameLength.txt' is incorrect! " && exit 1)
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echo ">>> Test finished successfully"
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exit 0
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