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https://github.com/MillironX/nf-core_modules.git
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add tests
This commit is contained in:
Matthias De Smet
parent
d6a0238cd1
commit
4da143ce62
4 changed files with 84 additions and 18 deletions
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@ -16,3 +16,14 @@ workflow test_picard_collecthsmetrics {
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PICARD_COLLECTHSMETRICS ( input, fasta, fai, bait_intervals, target_intervals )
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}
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workflow test_picard_collecthsmetrics_nofasta {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) ]
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bait_intervals = file(params.test_data['sarscov2']['genome']['baits_interval_list'], checkIfExists: true)
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target_intervals = file(params.test_data['sarscov2']['genome']['targets_interval_list'], checkIfExists: true)
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PICARD_COLLECTHSMETRICS ( input, [], [], bait_intervals, target_intervals )
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}
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@ -1,8 +1,17 @@
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- name: picard collecthsmetrics test_picard_collecthsmetrics
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command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
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command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
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tags:
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- picard
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- picard/collecthsmetrics
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- picard
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files:
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# The file can't be md5'd consistently
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- path: output/picard/test.CollectHsMetrics.coverage_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- name: picard collecthsmetrics test_picard_collecthsmetrics_nofasta
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command: nextflow run ./tests/modules/picard/collecthsmetrics -entry test_picard_collecthsmetrics_nofasta -c ./tests/config/nextflow.config -c ./tests/modules/picard/collecthsmetrics/nextflow.config
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tags:
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- picard/collecthsmetrics
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- picard
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files:
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- path: output/picard/test.CollectHsMetrics.coverage_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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@ -5,10 +5,20 @@ nextflow.enable.dsl = 2
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include { PICARD_COLLECTMULTIPLEMETRICS } from '../../../../modules/picard/collectmultiplemetrics/main.nf'
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workflow test_picard_collectmultiplemetrics {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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PICARD_COLLECTMULTIPLEMETRICS ( input, fasta )
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}
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workflow test_picard_collectmultiplemetrics_nofasta {
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input = [
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[ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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PICARD_COLLECTMULTIPLEMETRICS ( input, [] )
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}
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@ -1,17 +1,53 @@
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- name: picard collectmultiplemetrics
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command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
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- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics
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command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
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tags:
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- picard
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- picard/collectmultiplemetrics
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files:
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# These can't be md5'd consistently
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- path: ./output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.insert_size_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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- path: ./output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
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- path: ./output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
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- path: ./output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
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- path: ./output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
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- path: ./output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
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- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- name: picard collectmultiplemetrics test_picard_collectmultiplemetrics_nofasta
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command: nextflow run ./tests/modules/picard/collectmultiplemetrics -entry test_picard_collectmultiplemetrics_nofasta -c ./tests/config/nextflow.config -c ./tests/modules/picard/collectmultiplemetrics/nextflow.config
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tags:
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- picard
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- picard/collectmultiplemetrics
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files:
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- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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- path: output/picard/test.CollectMultipleMetrics.read_length_histogram.pdf
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contains: '[ # TODO nf-core: file md5sum was variable, please replace this text with a string found in the file instead ]'
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