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nf-core_modules/tests/modules/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
Rename software/ directory to modules/ to re-organise module structure (#567) * Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
2021-07-07 09:10:18 +00:00
include { STRELKA_GERMLINE } from '../../../../modules/strelka/germline/main.nf' addParams( options: [:] )
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
workflow test_strelka_germline {
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
input = [
Modules TLC (#551) * Modules TLC * Fix all the tests
2021-07-01 15:13:01 +00:00
[ id:'test'], // meta map
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
Modules TLC (#551) * Modules TLC * Fix all the tests
2021-07-01 15:13:01 +00:00
]
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
target_bed = []
target_bed_tbi = []
STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
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 {
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
input = [
Modules TLC (#551) * Modules TLC * Fix all the tests
2021-07-01 15:13:01 +00:00
[ id:'test'], // meta map
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true),
Modules TLC (#551) * Modules TLC * Fix all the tests
2021-07-01 15:13:01 +00:00
]
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)
target_bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)
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
Add Manta/somatic module + (fix tiny strelka params problem, i know bad practice :( ) (#912) * remove params statement * add manta/somatic module * fix strelka target bed thing * removing checksums should make this pass * Update modules/manta/somatic/main.nf Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com> * fix indentation Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
2021-10-27 14:14:52 +00:00
STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi )
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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