53 lines
1.6 KiB
Bash
Executable File
53 lines
1.6 KiB
Bash
Executable File
#!/usr/bin/env bash
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# A couple of simple tests with different combinations of CLI options
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if [[ "$#" -ne 1 ]]; then
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echo "Please supply path to out_dir"
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exit 1
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fi
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SCRIPT_DIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
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cd $SCRIPT_DIR;
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singledir="test_data/fastq"
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multisampledir="test_data/demultiplexed_fastq"
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echo $singledir
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echo $multisampledir
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results=()
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# Test1 single sample
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OUTPUT=$1/test1;
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nextflow run . --fastq $singledir --ref_genome test_data/SIRV_150601a.fasta \
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--ref_annotation test_data/SIRV_isofroms.gtf -profile conda --out_dir ${OUTPUT} -w ${OUTPUT}/workspace -resume;
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results+=("test1: $?")
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# Test2 multiple samples demultiplexed
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OUTPUT=$1/test2;
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nextflow run . --fastq $multisampledir --ref_genome test_data/SIRV_150601a.fasta \
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--ref_annotation test_data/SIRV_isofroms.gtf -profile conda --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
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--sample_sheet test_data/sample_sheet -resume;
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results+=("test2: $?")
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# Test3 single sample. No reference annotation
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OUTPUT=$1/test3;
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nextflow run . --fastq $singledir --ref_genome test_data/SIRV_150601a.fasta \
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-profile conda --out_dir ${OUTPUT} -w ${OUTPUT}/workspace -resume;
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results+=("test3: $?")
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# Test4 single sample. force split_bam to make multiple alignment bundles
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OUTPUT=$1/test4;
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nextflow run . --fastq $singledir --ref_genome test_data/SIRV_150601a.fasta \
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--ref_annotation test_data/SIRV_isofroms.gtf -profile conda --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
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--bundle_min_reads 5 -resume;
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results+=("test4: $?")
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echo "Exit status codes for each test"
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for value in "${results[@]}"; do
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echo "${value}"
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done |