73 lines
2.6 KiB
Bash
73 lines
2.6 KiB
Bash
#!/usr/bin/env bash
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# A few simple tests with different combinations of CLI options
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# Run from within an appropriate active conda environment
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if [[ "$#" -lt 1 ]]; then
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echo "usage: tests.sh <outdir> [nextflow.config]"
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exit 1
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fi
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if [[ "$#" -eq 1 ]]; then
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config=''
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fi
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if [[ "$#" -eq 2 ]]; then
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config="-c $2";
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fi
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SCRIPT_DIR="$( 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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# This is for when using SIRV dataset with non-canonical spice junctions
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#"--minimap2_opts '-uf --splice-flank=no'"
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results=()
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OUTPUT=$1/denovo_multi_sample_no_ref_genome;
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nextflow run . --fastq $multisampledir $config --denovo --ref_genome test_data/SIRV_150601a.fasta -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
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--sample_sheet test_data/sample_sheet -resume;
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r=$?
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results+=("$(basename $OUTPUT): $r")
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OUTPUT=$1/denovo_single;
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nextflow run . --fastq $singledir $config --denovo --ref_genome test_data/SIRV_150601a.fasta -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
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--sample_sheet test_data/sample_sheet -resume;
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r=$?
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results+=("$(basename $OUTPUT): $r")
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# Reference based tests
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OUTPUT=$1/reference_single_dir;
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nextflow run . --fastq $singledir $config --ref_genome test_data/SIRV_150601a.fasta --minimap2_opts '-uf --splice-flank=no' \
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--ref_annotation test_data/SIRV_isofroms.gtf -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace -resume;
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r=$?
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results+=("$(basename $OUTPUT): $r")
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OUTPUT=$1/multiple_samples;
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nextflow run . --fastq $multisampledir $config --ref_genome test_data/SIRV_150601a.fasta --minimap2_opts '-uf --splice-flank=no'\
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--ref_annotation test_data/SIRV_isofroms.gtf -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
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--sample_sheet test_data/sample_sheet -resume;
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r=$?
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results+=("$(basename $OUTPUT): $r")
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OUTPUT=$1/reference_no_ref_annotation;
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nextflow run . --fastq $singledir $config --ref_genome test_data/SIRV_150601a.fasta --minimap2_opts '-uf --splice-flank=no'\
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-profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace -resume;
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r=$?
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results+=("$(basename $OUTPUT): $r")
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# Force split_bam to make multiple alignment bundles
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OUTPUT=$1/reference_frce_split_bam;
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nextflow run . --fastq $singledir $config --ref_genome test_data/SIRV_150601a.fasta --minimap2_opts '-uf --splice-flank=no'\
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--ref_annotation test_data/SIRV_isofroms.gtf -profile local --out_dir ${OUTPUT} -w ${OUTPUT}/workspace \
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--bundle_min_reads 5 -resume;
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r=$?
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results+=("$(basename $OUTPUT): $r")
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echo "Exit status codes for each test"
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for value in "${results[@]}"; do
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echo "${value}"
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done |