CI
50e78b4b9a
Build pipeline: viash-hub.rnaseq.v0.1-gnwkh
Source commit: fd0354dae8
Source message: Point to new assets dir
30 lines
937 B
Bash
30 lines
937 B
Bash
#!/bin/bash
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gunzip "$meta_resources_dir/hg19_RefSeq.bed.gz"
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# define input and output for script
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input_bam="$meta_resources_dir/test.paired_end.sorted.bam"
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input_bed="$meta_resources_dir/test.bed"
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output_plot="junction_saturation_plot.pdf"
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output_plot_r="junction_saturation_plot.r"
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# run executable and test
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echo "> Running $meta_functionality_name"
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"$meta_executable" \
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--input "$input_bam" \
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--refgene "$input_bed" \
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--output_plot_r "$output_plot_r" \
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--output_plot "$output_plot"
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exit_code=$?
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[[ $exit_code != 0 ]] && echo "Non zero exit code: $exit_code" && exit 1
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echo ">> asserting all output files were created"
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[ ! -f "$output_plot_r" ] && echo "$output_plot_r was not created" && exit 1
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[ ! -s "$output_plot_r" ] && echo "$output_plot_r is empty" && exit 1
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[ ! -f "$output_plot" ] && echo "$output_plot was not created" && exit 1
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[ ! -s "$output_plot" ] && echo "$output_plot is empty" && exit 1
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exit 0 |