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priesgopriesgo
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make tests work again
1 parent 7d08e42 commit a4001c3

12 files changed

Lines changed: 55 additions & 51 deletions

‎Makefile‎

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@@ -3,6 +3,8 @@ SHELL := /bin/bash
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all : clean test
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.PHONY: all test clean
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clean:
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rm -rf output
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rm -rf work

‎test/data/test_bams.txt‎

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tumor_normal primary:/home/priesgo/src/github/tronflow-variant-normalization/test_data/TESTX_S1_L001.bam
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tumor_normal normal:/home/priesgo/src/github/tronflow-variant-normalization/test_data/TESTX_S1_L002.bam
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single_sample tumor:/home/priesgo/src/github/tronflow-variant-normalization/test_data/TESTX_S1_L001.bam
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single_sample tumor:/home/priesgo/src/github/tronflow-variant-normalization/test_data/TESTX_S1_L002.bam
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single_sample normal:/home/priesgo/src/github/tronflow-variant-normalization/test_data/TESTX_S1_L001.bam
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single_sample normal:/home/priesgo/src/github/tronflow-variant-normalization/test_data/TESTX_S1_L002.bam
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tumor_normal primary:/home/priesgo/src/github/tronflow-variant-normalization/test/data/TESTX_S1_L001.bam
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tumor_normal normal:/home/priesgo/src/github/tronflow-variant-normalization/test/data/TESTX_S1_L002.bam
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single_sample tumor:/home/priesgo/src/github/tronflow-variant-normalization/test/data/TESTX_S1_L001.bam
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single_sample tumor:/home/priesgo/src/github/tronflow-variant-normalization/test/data/TESTX_S1_L002.bam
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single_sample normal:/home/priesgo/src/github/tronflow-variant-normalization/test/data/TESTX_S1_L001.bam
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single_sample normal:/home/priesgo/src/github/tronflow-variant-normalization/test/data/TESTX_S1_L002.bam

‎test/data/test_input.txt‎

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tumor_normal test_data/test_tumor_normal.vcf
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single_sample test_data/test_single_sample.vcf
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tumor_normal test/data/test_tumor_normal.vcf
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single_sample test/data/test_single_sample.vcf

‎test/data/test_input_no_ad.txt‎

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sample_no_ad test_data/test_no_ad.vcf
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sample_no_ad test/data/test_no_ad.vcf

‎test/scripts/run_test_1.sh‎

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source test/scripts/assert.sh
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output_folder=test/output/test1
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nextflow main.nf -profile test,conda --output $output_folder
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test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 1 output file!"; exit 1; }
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test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 1 output file!"; exit 1; }
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assert_eq `wc -l $output_folder/single_sample/single_sample.normalized.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"

‎test/scripts/run_test_10.sh‎

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source test/scripts/assert.sh
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output_folder=test/output/test10
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echo -e "tumor_normal\tprimary:"`pwd`"/test/data/TESTX_S1_L001.bam" > test_data/test_bams.txt
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echo -e "tumor_normal\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "tumor_normal\tprimary:"`pwd`"/test/data/TESTX_S1_L001.bam" > test/data/test_bams.txt
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echo -e "tumor_normal\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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nextflow main.nf -profile test,conda --output $output_folder --input_bams test_data/test_bams.txt --skip_normalization
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nextflow main.nf -profile test,conda --output $output_folder --input_bams test/data/test_bams.txt --skip_normalization
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test -s $output_folder/single_sample/single_sample.filtered_multiallelics.vcf || { echo "Missing test 10 output file!"; exit 1; }
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test -s $output_folder/tumor_normal/tumor_normal.filtered_multiallelics.vcf || { echo "Missing test 10 output file!"; exit 1; }

‎test/scripts/run_test_11.sh‎

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output_folder=test/output/test11
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# build input BAMs file
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echo -e "tumor_normal\tprimary:"`pwd`"/test/data/TESTX_S1_L001.bam" > test_data/test_bams.txt
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echo -e "tumor_normal\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "tumor_normal\tprimary:"`pwd`"/test/data/TESTX_S1_L001.bam" > test/data/test_bams.txt
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echo -e "tumor_normal\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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# build input purities file
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echo -e "tumor_normal\tprimary:0.5" > test_data/test_purities.txt
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echo -e "tumor_normal\tnormal:0.6" >> test_data/test_purities.txt
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echo -e "single_sample\ttumor:0.7" >> test_data/test_purities.txt
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echo -e "single_sample\tnormal:0.8" >> test_data/test_purities.txt
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echo -e "tumor_normal\tprimary:0.5" > test/data/test_purities.txt
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echo -e "tumor_normal\tnormal:0.6" >> test/data/test_purities.txt
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echo -e "single_sample\ttumor:0.7" >> test/data/test_purities.txt
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echo -e "single_sample\tnormal:0.8" >> test/data/test_purities.txt
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nextflow main.nf -profile test,conda --output $output_folder \
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--input_bams test_data/test_bams.txt \
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--input_purities test_data/test_purities.txt \
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--input_bams test/data/test_bams.txt \
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--input_purities test/data/test_purities.txt \
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--skip_normalization
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# test output files

‎test/scripts/run_test_4.sh‎

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source test/scripts/assert.sh
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output_folder=test/output/test4
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nextflow main.nf -profile test,conda --input_vcfs test_data/test_input_no_ad.txt --output $output_folder
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nextflow main.nf -profile test,conda --input_vcfs test/data/test_input_no_ad.txt --output $output_folder
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test -s $output_folder/sample_no_ad/sample_no_ad.normalized.vcf || { echo "Missing test 4 output file!"; exit 1; }
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assert_eq `wc -l $output_folder/sample_no_ad/sample_no_ad.normalized.vcf | cut -d' ' -f 1` 52 "Wrong number of variants"

‎test/scripts/run_test_5.sh‎

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source test/scripts/assert.sh
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output_folder=test/output/test5
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nextflow main.nf -profile test,conda --output $output_folder --input_vcfs false --input_vcf test_data/test_single_sample.vcf
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nextflow main.nf -profile test,conda --output $output_folder --input_vcfs false --input_vcf test/data/test_single_sample.vcf
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test -s $output_folder/test_single_sample/test_single_sample.normalized.vcf || { echo "Missing test 4 output file!"; exit 1; }
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assert_eq `wc -l $output_folder/test_single_sample/test_single_sample.normalized.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"

‎test/scripts/run_test_6.sh‎

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output_folder=test/output/test6
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echo -e "tumor_normal\tprimary:"`pwd`"/test/data/TESTX_S1_L001.bam" > test_data/test_bams.txt
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echo -e "tumor_normal\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
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echo -e "tumor_normal\tprimary:"`pwd`"/test/data/TESTX_S1_L001.bam" > test/data/test_bams.txt
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echo -e "tumor_normal\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
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echo -e "single_sample\ttumor:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L001.bam" >> test/data/test_bams.txt
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echo -e "single_sample\tnormal:"`pwd`"/test/data/TESTX_S1_L002.bam" >> test/data/test_bams.txt
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# run
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nextflow main.nf -profile test,conda --output $output_folder --input_bams test_data/test_bams.txt
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nextflow main.nf -profile test,conda --output $output_folder --input_bams test/data/test_bams.txt
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# check results
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test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 6 output file!"; exit 1; }

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