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043a7d1e3c
* remove deprecated test tags * fix bowtie, gatk4/applybsqr * fix gatk4 baserecalibrator * fixed shovill * fixed yara/mapper * fixed kallistobustools/ref paths
38 lines
1.4 KiB
YAML
38 lines
1.4 KiB
YAML
- name: fastp test_fastp_single_end
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command: nextflow run tests/software/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
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- "single end (151 cycles)"
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- path: output/fastp/test.fastp.log
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contains:
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- "Q20 bases: 12922(92.9841%)"
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- "reads passed filter: 99"
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- path: output/fastp/test.trim.fastq.gz
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md5sum: e2257263668dc8a75d95475099fb472d
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- path: output/fastp/test.fastp.json
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md5sum: e0d856ebb3da9e4462c3ce9683efe01d
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- name: fastp test_fastp_paired_end
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command: nextflow run tests/software/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
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tags:
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- fastp
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files:
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- path: output/fastp/test.fastp.html
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contains:
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- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
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- "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
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- path: output/fastp/test.fastp.log
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contains:
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- "No adapter detected for read1"
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- "Q30 bases: 12281(88.3716%)"
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- path: output/fastp/test.fastp.json
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contains:
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- '"passed_filter_reads": 198'
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- path: output/fastp/test_1.trim.fastq.gz
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md5sum: e2257263668dc8a75d95475099fb472d
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- path: output/fastp/test_2.trim.fastq.gz
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md5sum: 9eff7203596580cc5e42aceab4a469df
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