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modify fastp tests (#367)

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Co-authored-by: Gregor Sturm <mail@gregor-sturm.de>
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Maxime Borry 2021-03-24 17:08:59 +01:00 committed by GitHub
parent 86df111707
commit cfc94b96dd
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1 changed files with 34 additions and 19 deletions
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53
tests/software/fastp/test.yml
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@ -1,25 +1,40 @@
- name: fastp single-end - name: fastp test_fastp_single_end
command: nextflow run ./tests/software/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config command: nextflow run tests/software/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
tags: tags:
- fastp
- fastp_single_end - fastp_single_end
files:
- path: ./output/fastp/test.fastp.html
- path: ./output/fastp/test.fastp.log
- path: ./output/fastp/test.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d
- path: ./output/fastp/test.fastp.json
- name: fastp paired-end
command: nextflow run ./tests/software/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config
tags:
- fastp - fastp
- fastp_paired_end
files: files:
- path: ./output/fastp/test.fastp.html - path: output/fastp/test.fastp.html
- path: ./output/fastp/test.fastp.log contains:
- path: ./output/fastp/test.fastp.json - "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
- path: ./output/fastp/test_1.trim.fastq.gz - "single end (151 cycles)"
- path: output/fastp/test.fastp.log
contains:
- "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 99"
- path: output/fastp/test.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d md5sum: e2257263668dc8a75d95475099fb472d
- path: ./output/fastp/test_2.trim.fastq.gz - path: output/fastp/test.fastp.json
md5sum: e0d856ebb3da9e4462c3ce9683efe01d
- name: fastp test_fastp_paired_end
command: nextflow run tests/software/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
tags:
- fastp_paired_end
- fastp
files:
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
- "The input has little adapter percentage (~0.000000%), probably it's trimmed before."
- path: output/fastp/test.fastp.log
contains:
- "No adapter detected for read1"
- "Q30 bases: 12281(88.3716%)"
- path: output/fastp/test.fastp.json
contains:
- '"passed_filter_reads": 198'
- path: output/fastp/test_1.trim.fastq.gz
md5sum: e2257263668dc8a75d95475099fb472d
- path: output/fastp/test_2.trim.fastq.gz
md5sum: 9eff7203596580cc5e42aceab4a469df md5sum: 9eff7203596580cc5e42aceab4a469df