2020-11-25 00:32:23 +00:00
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- name: Run picard mergesamfiles
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command: nextflow run ./tests/software/picard -profile docker -entry test_picard_mergesamfiles -c tests/config/nextflow.config
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tags:
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- picard
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- picard_mergesamfiles
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files:
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- path: output/picard/test.bam
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md5sum: a9c8a28d1aac362df5973ba2d9923f86
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2020-11-25 00:48:59 +00:00
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- name: Run picard collectmultiplemetrics
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command: nextflow run ./tests/software/picard -profile docker -entry test_picard_collectmultiplemetrics -c tests/config/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.base_distribution_by_cycle.pdf
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- path: output/picard/test.CollectMultipleMetrics.base_distribution_by_cycle_metrics
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- path: output/picard/test.CollectMultipleMetrics.insert_size_histogram.pdf
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- path: output/picard/test.CollectMultipleMetrics.insert_size_metrics
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- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle.pdf
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- path: output/picard/test.CollectMultipleMetrics.quality_by_cycle_metrics
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- path: output/picard/test.CollectMultipleMetrics.quality_distribution.pdf
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- path: output/picard/test.CollectMultipleMetrics.quality_distribution_metrics
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2020-11-25 01:38:10 +00:00
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- name: Run picard MarkDuplicates
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command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates -c tests/config/nextflow.config
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tags:
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- picard
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- picard_markduplicates
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files:
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- path: output/picard/test.MarkDuplicates.metrics.txt
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- path: output/picard/test.bam
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2020-12-14 00:44:49 +00:00
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md5sum: 0ed0bfc94069380334ccd595f6d8207c
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2020-11-25 01:38:49 +00:00
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- name: Run picard MarkDuplicates without a sorted bam file so it fails
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command: nextflow run ./tests/software/picard -profile docker -entry test_picard_markduplicates_not_sorted -c tests/config/nextflow.config
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tags:
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- picard
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- picard_markduplicates
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- should fail
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exit_code: 1
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