mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
43 lines
1.9 KiB
YAML
43 lines
1.9 KiB
YAML
- name: Run picard mergesamfiles
|
|
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config
|
|
tags:
|
|
- picard
|
|
- picard_mergesamfiles
|
|
files:
|
|
- path: output/picard/test.bam
|
|
md5sum: a9c8a28d1aac362df5973ba2d9923f86
|
|
|
|
- name: Run picard collectmultiplemetrics
|
|
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/nextflow.config
|
|
tags:
|
|
- picard
|
|
- picard_collectmultiplemetrics
|
|
files:
|
|
# These can't be md5'd consistently
|
|
- path: output/picard/test.CollectMultipleMetrics.alignment_summary_metrics
|
|
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle.pdf
|
|
- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
|
|
- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
|
|
- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
|
|
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
|
|
- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
|
|
- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
|
|
- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
|
|
|
|
- name: Run picard MarkDuplicates
|
|
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates -c tests/config/nextflow.config
|
|
tags:
|
|
- picard
|
|
- picard_markduplicates
|
|
files:
|
|
- path: output/picard/test.MarkDuplicates.metrics.txt
|
|
- path: output/picard/test.bam
|
|
md5sum: 0ed0bfc94069380334ccd595f6d8207c
|
|
|
|
- name: Run picard MarkDuplicates without a sorted bam file so it fails
|
|
command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
|
|
tags:
|
|
- picard
|
|
- picard_markduplicates
|
|
- should fail
|
|
exit_code: 1
|