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nf-core_modules/tests/software/strelka/germline/main.nf

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Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STRELKA_GERMLINE } from '../../../../software/strelka/germline/main.nf' addParams( options: [:] )
workflow test_strelka_germline {
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
2021-03-24 09:53:41 +00:00
input = [ [ id:'test'], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
targets = []
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
2021-03-24 09:53:41 +00:00
STRELKA_GERMLINE ( input, fasta, fai, targets )
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
}
Re-organise all test data (#354) * Re-organise all test data * Fix ECLint * Fix ECLint agaaainn * Now is not the time EClint
2021-03-24 09:53:41 +00:00
workflow test_strelka_germline_target_bed {
input = [ [ id:'test'], // meta map
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/bam/test_paired_end.sorted.bam.bai", checkIfExists: true)
]
fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
fai = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
targets = file("${launchDir}/tests/data/genomics/sarscov2/genome/bed/test.bed", checkIfExists: true)
STRELKA_GERMLINE ( input, fasta, fai, targets )
Strelka germline (#340) * nf-core template created * boilerplate and sarek_dsl2 code merged * adding an option to give it args * bai got away * seperating vcf files and vcf index files into seperate streams * some minor spacefixes * adding standard information about the module * removing typos * some basic tests based on tiddit tests * removed the bed parameter, should be provided via options.args instead * removing typos * adding indexed bam file instead * Adding changing out fasta with reference to deal with empty fasta input * adding the correct fasta * removing the empty test * adding the correct data to the testoutput and removing the md5sum since it constantly changes * adding target_bed to input * adding info on target bed * adding target bed to test * adding more files to the test * adding meta for target bed test * adding a test for target_bed * typo * fixing pytest with master
2021-03-24 05:07:29 +00:00
}
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