CI
5fc8f64fcb
Build pipeline: viash-hub.biobox.update-busco-bsvnf
Source commit: 1ca6dec48e
Source message: Typo
74 lines
2.5 KiB
Bash
74 lines
2.5 KiB
Bash
#!/bin/bash
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set -e
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## VIASH START
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meta_executable="target/docker/fastp/fastp"
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meta_resources_dir="src/fastp"
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## VIASH END
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#########################################################################################
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mkdir fastp_se
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cd fastp_se
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echo "> Run fastp on SE"
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"$meta_executable" \
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--in1 "$meta_resources_dir/test_data/se/a.fastq" \
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--out1 "trimmed.fastq" \
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--failed_out "failed.fastq" \
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--json "report.json" \
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--html "report.html" \
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--adapter_sequence ACGGCTAGCTA
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echo ">> Check if output exists"
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[ ! -f "trimmed.fastq" ] && echo ">> trimmed.fastq does not exist" && exit 1
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[ ! -f "failed.fastq" ] && echo ">> failed.fastq does not exist" && exit 1
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[ ! -f "report.json" ] && echo ">> report.json does not exist" && exit 1
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[ ! -f "report.html" ] && echo ">> report.html does not exist" && exit 1
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#########################################################################################
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cd ..
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mkdir fastp_pe_minimal
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cd fastp_pe_minimal
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echo ">> Run fastp on PE with minimal parameters"
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"$meta_executable" \
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--in1 "$meta_resources_dir/test_data/pe/a.1.fastq" \
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--in2 "$meta_resources_dir/test_data/pe/a.2.fastq" \
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--out1 "trimmed_1.fastq" \
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--out2 "trimmed_2.fastq"
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echo ">> Check if output exists"
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[ ! -f "trimmed_1.fastq" ] && echo ">> trimmed_1.fastq does not exist" && exit 1
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[ ! -f "trimmed_2.fastq" ] && echo ">> trimmed_2.fastq does not exist" && exit 1
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#########################################################################################
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cd ..
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mkdir fastp_pe_many
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cd fastp_pe_many
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echo ">> Run fastp on PE with many parameters"
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"$meta_executable" \
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--in1 "$meta_resources_dir/test_data/pe/a.1.fastq" \
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--in2 "$meta_resources_dir/test_data/pe/a.2.fastq" \
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--out1 "trimmed_1.fastq" \
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--out2 "trimmed_2.fastq" \
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--failed_out "failed.fastq" \
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--json "report.json" \
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--html "report.html" \
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--adapter_sequence ACGGCTAGCTA \
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--adapter_sequence_r2 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC \
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--merge \
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--merged_out "merged.fastq"
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echo ">> Check if output exists"
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[ ! -f "trimmed_1.fastq" ] && echo ">> trimmed_1.fastq does not exist" && exit 1
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[ ! -f "trimmed_2.fastq" ] && echo ">> trimmed_2.fastq does not exist" && exit 1
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[ ! -f "failed.fastq" ] && echo ">> failed.fastq does not exist" && exit 1
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[ ! -f "report.json" ] && echo ">> report.json does not exist" && exit 1
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[ ! -f "report.html" ] && echo ">> report.html does not exist" && exit 1
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[ ! -f "merged.fastq" ] && echo ">> merged.fastq does not exist" && exit 1
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#########################################################################################
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echo "> Test successful" |