millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 11:08:17 +00:00
Code Issues Releases Packages Activity

add tests

Browse source
This commit is contained in:
Matthias De Smet 2022-05-22 06:43:48 +02:00
parent d6a0238cd1
commit 4da143ce62
4 changed files with 84 additions and 18 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

11
tests/modules/picard/collecthsmetrics/main.nf
View file

@ -16,3 +16,14 @@ workflow test_picard_collecthsmetrics {
PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals ) PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
} }
workflow test_picard_collecthsmetrics_nofasta {
input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
PICARD_COLLECTHSMETRICS ( input, [], [], bait_intervals, target_intervals )
}

15
tests/modules/picard/collecthsmetrics/test.yml
View file

@ -1,8 +1,17 @@
- name: picard collecthsmetrics test_picard_collecthsmetrics - name: picard collecthsmetrics test_picard_collecthsmetrics
command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
tags: tags:
- picard
- picard/collecthsmetrics - picard/collecthsmetrics
- picard
files: files:
# The file can't be md5'd consistently
- path: output/picard/test.CollectHsMetrics.coverage_metrics - path: output/picard/test.CollectHsMetrics.coverage_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- name: picard collecthsmetrics test_picard_collecthsmetrics_nofasta
command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics_nofasta -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
tags:
- picard/collecthsmetrics
- picard
files:
- path: output/picard/test.CollectHsMetrics.coverage_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'

14
tests/modules/picard/collectmultiplemetrics/main.nf
View file

@ -5,10 +5,20 @@ nextflow.enable.dsl = 2
include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf' include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
workflow test_picard_collectmultiplemetrics { workflow test_picard_collectmultiplemetrics {
input = [ [ id:'test', single_end:false ], // meta map input = [
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
] ]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
PICARD_COLLECTMULTIPLEMETRICS ( input, fasta ) PICARD_COLLECTMULTIPLEMETRICS ( input, fasta )
} }
workflow test_picard_collectmultiplemetrics_nofasta {
input = [
[ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
]
PICARD_COLLECTMULTIPLEMETRICS ( input, [] )
}

62
tests/modules/picard/collectmultiplemetrics/test.yml
View file

@ -1,17 +1,53 @@
- name: picard collectmultiplemetrics - name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
tags: tags:
- picard - picard
- picard/collectmultiplemetrics - picard/collectmultiplemetrics
files: files:
# These can't be md5'd consistently - path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
- path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics - path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf - path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution.pdf contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: ./output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf - path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: ./output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf - path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
tags:
- picard
- picard/collectmultiplemetrics
files:
- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
- path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'