CI
6df312e701
Build pipeline: viash-hub.biobox.gatk-applybqsrspark-jpq6r
Source commit: c4ea23a0f5
Source message: Add RSEM prepare reference component (#89)
* initial commit
* incorporaate some requested changes
* update test
* change argument reference_fasta_files to multiple true and update docker setup
* Update src/rsem/rsem_prepare_reference/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/rsem/rsem_prepare_reference/config.vsh.yaml
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* Update src/rsem/rsem_prepare_reference/script.sh
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
* set multiple true
* update changelog
* Apply suggestions from code review
* fix script
---------
Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
341 lines
11 KiB
Bash
341 lines
11 KiB
Bash
#!/bin/bash
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# exit on error
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set -e
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## VIASH START
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meta_executable="target/executable/bedtools/bedtools_intersect/bedtools_intersect"
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meta_resources_dir="src/bedtools/bedtools_intersect"
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## VIASH END
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#############################################
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# helper functions
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assert_file_exists() {
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[ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
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}
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assert_file_not_empty() {
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[ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
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}
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assert_file_contains() {
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grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
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}
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assert_identical_content() {
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diff -a "$2" "$1" \
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|| (echo "Files are not identical!" && exit 1)
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}
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#############################################
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# Create directories for tests
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echo "Creating Test Data..."
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mkdir -p test_data
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# Create and populate featuresA.bed
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printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/featuresA.bed"
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# Create and populate featuresB.bed
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printf "chr1\t180\t280\nchr1\t290\t390\nchr1\t500\t600\n" > "test_data/featuresB.bed"
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# Create and populate featuresC.bed
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printf "chr1\t120\t220\nchr1\t250\t350\nchr1\t500\t580\n" > "test_data/featuresC.bed"
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# Create and populate examples gff files
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# example1.gff
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printf "##gff-version 3\n" > "test_data/example1.gff"
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printf "chr1\t.\tgene\t1000\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/example1.gff"
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printf "chr1\t.\tmRNA\t1000\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/example1.gff"
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printf "chr1\t.\texon\t1000\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/example1.gff"
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printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/example1.gff"
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printf "chr1\t.\tCDS\t1000\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/example1.gff"
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printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/example1.gff"
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# example2.gff
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printf "##gff-version 3\n" > "test_data/example2.gff"
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printf "chr1\t.\tgene\t1200\t1800\t.\t-\t.\tID=gene2;Name=Gene2\n" >> "test_data/example2.gff"
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printf "chr1\t.\tmRNA\t1400\t2000\t.\t-\t.\tID=transcript2;Parent=gene2\n" >> "test_data/example2.gff"
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printf "chr1\t.\texon\t1400\t2000\t.\t-\t.\tID=exon3;Parent=transcript2\n" >> "test_data/example2.gff"
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printf "chr1\t.\texon\t1600\t2000\t.\t-\t.\tID=exon4;Parent=transcript2\n" >> "test_data/example2.gff"
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printf "chr1\t.\tCDS\t3000\t3200\t.\t-\t1\tID=cds3;Parent=transcript2\n" >> "test_data/example2.gff"
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printf "chr1\t.\tCDS\t3500\t3700\t.\t-\t0\tID=cds4;Parent=transcript2\n" >> "test_data/example2.gff"
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# Create and populate expected output files for different tests
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printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_default.bed"
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printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/expected_wa.bed"
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printf "chr1\t180\t200\tchr1\t180\t280\nchr1\t180\t250\tchr1\t180\t280\nchr1\t300\t390\tchr1\t290\t390\n" > "test_data/expected_wb.bed"
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printf "chr1\t100\t200\tchr1\t180\t280\nchr1\t150\t250\tchr1\t180\t280\nchr1\t300\t400\tchr1\t290\t390\n" > "test_data/expected_loj.bed"
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printf "chr1\t100\t200\tchr1\t180\t280\t20\nchr1\t150\t250\tchr1\t180\t280\t70\nchr1\t300\t400\tchr1\t290\t390\t90\n" > "test_data/expected_wo.bed"
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printf "chr1\t100\t200\nchr1\t150\t250\nchr1\t300\t400\n" > "test_data/expected_u.bed"
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printf "chr1\t100\t200\t1\nchr1\t150\t250\t1\nchr1\t300\t400\t1\n" > "test_data/expected_c.bed"
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printf "chr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f50.bed"
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printf "chr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f30.bed"
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printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_f10.bed"
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printf "chr1\t180\t200\nchr1\t180\t250\nchr1\t300\t390\n" > "test_data/expected_r.bed"
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printf "chr1\t180\t200\nchr1\t120\t200\nchr1\t180\t250\nchr1\t150\t220\nchr1\t300\t390\nchr1\t300\t350\n" > "test_data/expected_multiple.bed"
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# expected gff file
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printf "chr1\t.\tgene\t1200\t1800\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tgene\t1400\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tgene\t1400\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tgene\t1600\t2000\t.\t+\t.\tID=gene1;Name=Gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tmRNA\t1200\t1800\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tmRNA\t1400\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tmRNA\t1400\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tmRNA\t1600\t2000\t.\t+\t.\tID=transcript1;Parent=gene1\n" >> "test_data/expected.gff"
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printf "chr1\t.\texon\t1200\t1200\t.\t+\t.\tID=exon1;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\texon\t1500\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\texon\t1600\t1700\t.\t+\t.\tID=exon2;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tCDS\t1200\t1200\t.\t+\t0\tID=cds1;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tCDS\t1500\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
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printf "chr1\t.\tCDS\t1600\t1700\t.\t+\t2\tID=cds2;Parent=transcript1\n" >> "test_data/expected.gff"
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# Test 1: Default intersect
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mkdir test1
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cd test1
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echo "> Run bedtools_intersect on BED files with default intersect"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed"
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_default.bed"
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echo "- test1 succeeded -"
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cd ..
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# Test 2: Write A option
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mkdir test2
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cd test2
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echo "> Run bedtools_intersect on BED files with -wa option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--write_a
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_wa.bed"
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echo "- test2 succeeded -"
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cd ..
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# Test 3: -wb option
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mkdir test3
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cd test3
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echo "> Run bedtools_intersect on BED files with -wb option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--write_b
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_wb.bed"
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echo "- test3 succeeded -"
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cd ..
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# Test 4: -loj option
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mkdir test4
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cd test4
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echo "> Run bedtools_intersect on BED files with -loj option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--left_outer_join
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_loj.bed"
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echo "- test4 succeeded -"
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cd ..
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# Test 5: -wo option
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mkdir test5
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cd test5
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echo "> Run bedtools_intersect on BED files with -wo option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--write_overlap
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_wo.bed"
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echo "- test5 succeeded -"
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cd ..
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# Test 6: -u option
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mkdir test6
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cd test6
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echo "> Run bedtools_intersect on BED files with -u option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--report_A_if_no_overlap true
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_u.bed"
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echo "- test6 succeeded -"
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cd ..
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# Test 7: -c option
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mkdir test7
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cd test7
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echo "> Run bedtools_intersect on BED files with -c option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--number_of_overlaps_A true
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_c.bed"
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echo "- test7 succeeded -"
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cd ..
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# Test 8: -f 0.50 option
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mkdir test8
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cd test8
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echo "> Run bedtools_intersect on BED files with -f 0.50 option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--min_overlap_A 0.50
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_f50.bed"
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echo "- test8 succeeded -"
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cd ..
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# Test 9: -f 0.30 option
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mkdir test9
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cd test9
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echo "> Run bedtools_intersect on BED files with -f 0.30 option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--min_overlap_A 0.30
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_f30.bed"
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echo "- test9 succeeded -"
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cd ..
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# Test 10: -f 0.10 option
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mkdir test10
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cd test10
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echo "> Run bedtools_intersect on BED files with -f 0.10 option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--min_overlap_A 0.10
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_f10.bed"
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echo "- test10 succeeded -"
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cd ..
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# Test 11: -r option
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mkdir test11
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cd test11
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echo "> Run bedtools_intersect on BED files with -r option"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--output "output.bed" \
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--reciprocal_overlap true
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_r.bed"
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echo "- test11 succeeded -"
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cd ..
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# Test 12: Multiple files
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mkdir test12
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cd test12
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echo "> Run bedtools_intersect on multiple BED files"
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"$meta_executable" \
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--input_a "../test_data/featuresA.bed" \
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--input_b "../test_data/featuresB.bed" \
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--input_b "../test_data/featuresC.bed" \
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--output "output.bed"
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected_multiple.bed"
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echo "- test12 succeeded -"
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cd ..
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# Test 13: VCF file format
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mkdir test13
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cd test13
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echo "> Run bedtools_intersect on GFF files"
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"$meta_executable" \
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--input_a "../test_data/example1.gff" \
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--input_b "../test_data/example2.gff" \
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--output "output.bed"
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# checks
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assert_file_exists "output.bed"
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assert_file_not_empty "output.bed"
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assert_identical_content "output.bed" "../test_data/expected.gff"
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echo "- test13 succeeded -"
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cd ..
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echo "---- All tests succeeded! ----"
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exit 0
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