nf-core_modules/software/fastqc/test/deprecated/main.nf

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2020-08-06 23:36:05 +00:00
#!/usr/bin/env nextflow
import checksum
nextflow.preview.dsl = 2
params.out_dir = "test_output"
params.fastqc_args = ''
params.publish_dir_mode = "copy"
include { FASTQC } from '../main.nf'
/**
* Test if FASTQC runs with single-end data
*/
workflow test_single_end {
input_files = Channel.fromPath("${baseDir}/input/test_single_end.fastq.gz")
.map {f -> [f.name.replace(".fastq.gz", ""), true, f]}
FASTQC(input_files)
// test that the output looks as expected
FASTQC.out.html.map { name, is_single_end, html_file ->
html_hash = checksum.getMD5(new File("${html_file}"));
assert name == "test_single_end"
assert is_single_end == true
assert html_file.getName() == "test_single_end_fastqc.html"
// Hash seems to vary between local runs and GitHub Actions
// TODO: Might be solved when using Docker for tests?
// assert html_hash == "8ed68442ebb5b9706bf79b4f66701e15"
}
FASTQC.out.zip.map { name, is_single_end, zip_file ->
// NOTE: output zip files do not have a consistent hash
assert name == "test_single_end"
assert is_single_end == true
assert zip_file.getName() == "test_single_end_fastqc.zip"
}
}
/**
* Test if FASTQC runs with paired end data
*/
workflow test_paired_end {
input_files = Channel.fromFilePairs("input/test_R{1,2}.fastq.gz")
.map {f -> [f[0], false, f[1]]}
FASTQC(input_files)
// test that the output looks as expected
FASTQC.out.html.map { name, is_single_end, html_files ->
html_r1 = html_files[0]
html_r2 = html_files[1]
html_r1_hash = checksum.getMD5(new File("${html_r1}"));
html_r2_hash = checksum.getMD5(new File("${html_r2}"));
assert name == "test_R"
assert is_single_end == false
assert html_r1.getName() == "test_R_1_fastqc.html"
assert html_r2.getName() == "test_R_2_fastqc.html"
assert html_r1_hash == "082c13ce7163ea0f52a66b83cb57b0f0"
assert html_r2_hash == "4ff04ec8da77e3af512f03b8c09a9e04"
}
FASTQC.out.zip.map { name, is_single_end, zip_files ->
zip_r1 = zip_files[0]
zip_r2 = zip_files[1]
// NOTE: output zip files do not have a consistent hash
assert name == "test_R"
assert is_single_end == false
assert zip_r1.getName() == "test_R_1_fastqc.zip"
assert zip_r2.getName() == "test_R_2_fastqc.zip"
}
}
workflow {
test_single_end()
test_paired_end()
}