nf-core_modules/tests/modules/fastp/test.yml
James A. Fellows Yates 10502399ad
Replaced param with input val channel (#595)
* Replaced param with input val channel

* Apply suggestions from code review

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* Apply suggestions from code review (missed one)

* YAML lint

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
2021-07-21 10:00:48 +02:00

83 lines
3.2 KiB
YAML

- name: fastp test_fastp_single_end
command: nextflow run tests/modules/fastp -entry test_fastp_single_end -c tests/config/nextflow.config
tags:
- fastp
files:
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
- "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
- path: output/fastp/test.fastp.json
md5sum: e0d856ebb3da9e4462c3ce9683efe01d
- name: fastp test_fastp_paired_end
command: nextflow run tests/modules/fastp -entry test_fastp_paired_end -c tests/config/nextflow.config
tags:
- 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
- name: fastp test_fastp_single_end_trim_fail
command: nextflow run tests/modules/fastp -entry test_fastp_single_end_trim_fail -c tests/config/nextflow.config
tags:
- fastp
files:
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
- "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
- path: output/fastp/test.fastp.json
md5sum: ee65a46d6e59fa556f112727b8a902ce
- path: output/fastp/test.fail.fastq.gz
md5sum: de315d397c994d8e66bafc7a8dc11070
- name: fastp test_fastp_paired_end_trim_fail
command: nextflow run tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c tests/config/nextflow.config
tags:
- 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
- path: output/fastp/test_1.fail.fastq.gz
md5sum: e62ff0123a74adfc6903d59a449cbdb0
- path: output/fastp/test_2.fail.fastq.gz
md5sum: f52309b35a7c15cbd56a9c3906ef98a5