CI
1e77c47f20
Build pipeline: viash-hub.biobox.qualimap-nmgj2
Source commit: 58d7dacfc2
Source message: Update src/qualimap/qualimap_rnaseq/script.sh
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
112 lines
3.6 KiB
Bash
Executable File
112 lines
3.6 KiB
Bash
Executable File
#!/bin/bash
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## VIASH START
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## VIASH END
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set -e
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test_output_dir="${meta_resources_dir}/test_data/test_output"
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test_dir="${meta_resources_dir}/test_data"
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expected_output_dir="${meta_resources_dir}/test_data/output"
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mkdir -p "$test_output_dir"
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################################################################################
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echo "> Test 1 - Read annotation file, output GFF"
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"$meta_executable" \
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--expose_dups \
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--outfile "$test_output_dir/ann_simple.gff" \
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--input "$test_dir/sequence.gff3"
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echo ">> Check if output exists"
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[ ! -f "$test_output_dir/ann_simple.gff" ] \
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&& echo "Output file test_output/ann_simple.gff does not exist" && exit 1
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echo ">> Check if output is empty"
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[ ! -s "$test_output_dir/ann_simple.gff" ] \
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&& echo "Output file test_output/ann_simple.gff is empty" && exit 1
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echo ">> Compare output to expected output"
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# compare file expect lines starting with "#"
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diff <(grep -v "^#" "$expected_output_dir/ann_simple.gff") \
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<(grep -v "^#" "$test_output_dir/ann_simple.gff") || \
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(echo "Output file ann_simple.gff does not match expected output" && exit 1)
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################################################################################
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echo "> Test 2 - Read annotation file, output GTF"
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"$meta_executable" \
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--gtf_output \
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--outfile "$test_output_dir/annotation.gtf" \
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--input "$test_dir/sequence.gff3"
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echo ">> Check if output exists"
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[ ! -f "$test_output_dir/annotation.gtf" ] \
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&& echo "Output file test_output/annotation.gtf does not exist" && exit 1
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echo ">> Check if output is empty"
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[ ! -s "$test_output_dir/annotation.gtf" ] \
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&& echo "Output file test_output/annotation.gtf is empty" && exit 1
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echo ">> Compare output to expected output"
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diff "$expected_output_dir/annotation.gtf" "$test_output_dir/annotation.gtf" || \
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(echo "Output file annotation.gtf does not match expected output" && exit 1)
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################################################################################
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echo "> Test 3 - Generate fasta file from annotation file"
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"$meta_executable" \
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--genome "$test_dir/sequence.fasta" \
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--spliced_exons "$test_output_dir/transcripts.fa" \
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--outfile "$test_output_dir/output.gff" \
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--input "$test_dir/sequence.gff3"
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echo ">> Check if output exists"
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[ ! -f "$test_output_dir/transcripts.fa" ] \
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&& echo "Output file transcripts.fa does not exist" && exit 1
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echo ">> Check if output is empty"
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[ ! -s "$test_output_dir/transcripts.fa" ] \
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&& echo "Output file transcripts.fa is empty" && exit 1
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echo ">> Compare output to expected output"
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diff "$expected_output_dir/transcripts.fa" "$test_output_dir/transcripts.fa" || \
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(echo "Output file transcripts.fa does not match expected output" && exit 1)
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################################################################################
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echo "> Test 4 - Generate table from GFF annotation file"
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"$meta_executable" \
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--table @id,@chr,@start,@end,@strand,@exons,Name,gene,product \
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--outfile "$test_output_dir/annotation.tbl" \
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--input "$test_dir/sequence.gff3"
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echo ">> Check if output exists"
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[ ! -f "$test_output_dir/annotation.tbl" ] \
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&& echo "Output file test_output/annotation.tbl does not exist" && exit 1
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echo ">> Check if output is empty"
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[ ! -s "$test_output_dir/annotation.tbl" ] \
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&& echo "Output file test_output/annotation.tbl is empty" && exit 1
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echo ">> Compare output to expected output"
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diff "$expected_output_dir/annotation.tbl" "$test_output_dir/annotation.tbl" || \
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(echo "Output file annotation.tbl does not match expected output" && exit 1)
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################################################################################
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rm -r "$test_output_dir"
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echo "> All tests successful"
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exit 0
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