mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
9b51362a53
* Rename output from fastp module * UPdate tests * fix alignment * prettier * Update modules/fastp/main.nf Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> * apply review suggestion -sf * typo * update md5 * update md5 * try with human data * revert, human data also doesn't work * use contains instead Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
108 lines
4.2 KiB
YAML
108 lines
4.2 KiB
YAML
- name: fastp test_fastp_single_end
|
|
command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
|
|
tags:
|
|
- fastp
|
|
files:
|
|
- path: output/fastp/test.fastp.fastq.gz
|
|
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
|
|
- 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.json
|
|
md5sum: 7ee735cefb67f549dc857eefb9e7f123
|
|
- path: output/fastp/test.fastp.log
|
|
contains:
|
|
- "Q20 bases: 12922(92.9841%)"
|
|
- "reads passed filter: 99"
|
|
|
|
- name: fastp test_fastp_paired_end
|
|
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/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.json
|
|
contains:
|
|
- '"passed_filter_reads": 198'
|
|
- path: output/fastp/test.fastp.log
|
|
contains:
|
|
- "No adapter detected for read1"
|
|
- "Q30 bases: 12281(88.3716%)"
|
|
- path: output/fastp/test_1.fastp.fastq.gz
|
|
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
|
|
- path: output/fastp/test_2.fastp.fastq.gz
|
|
md5sum: 532b190fb4dc7b2277ee5cf1464e598c
|
|
|
|
- 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 -c ./tests/modules/fastp/nextflow.config
|
|
tags:
|
|
- fastp
|
|
files:
|
|
- path: output/fastp/test.fail.fastq.gz
|
|
md5sum: b57f2026eb259a0b0c0b3960c270258d
|
|
- path: output/fastp/test.fastp.fastq.gz
|
|
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
|
|
- 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.json
|
|
md5sum: feafc4181a2a61b4b52d9c2b59b419ad
|
|
- path: output/fastp/test.fastp.log
|
|
contains:
|
|
- "Q20 bases: 12922(92.9841%)"
|
|
- "reads passed filter: 99"
|
|
|
|
- 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 -c ./tests/modules/fastp/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.fail.fastq.gz
|
|
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
|
- path: output/fastp/test_1.fastp.fastq.gz
|
|
md5sum: 4ce5c2b4db68a743cb0635ce7da3b9a4
|
|
- path: output/fastp/test_2.fail.fastq.gz
|
|
md5sum: 72d0002841967676ac936d08746a9128
|
|
- path: output/fastp/test_2.fastp.fastq.gz
|
|
md5sum: 532b190fb4dc7b2277ee5cf1464e598c
|
|
|
|
- name: fastp test_fastp_paired_end_merged
|
|
command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
|
|
tags:
|
|
- fastp
|
|
files:
|
|
- path: output/fastp/test.fastp.html
|
|
contains:
|
|
- "<div id='After_filtering__merged__quality'>"
|
|
- path: output/fastp/test.fastp.json
|
|
contains:
|
|
- '"merged_and_filtered": {'
|
|
- '"total_reads": 75'
|
|
- '"total_bases": 13683'
|
|
- path: output/fastp/test.fastp.log
|
|
contains:
|
|
- "Merged and filtered:"
|
|
- "total reads: 75"
|
|
- "total bases: 13683"
|
|
- path: output/fastp/test.merged.fastq.gz
|
|
md5sum: 4955ca2c899729b17bd526d2626a8d73
|
|
- path: output/fastp/test_1.fastp.fastq.gz
|
|
md5sum: 4a03721ee252b7c6e81e007550e6ab63
|
|
- path: output/fastp/test_2.fastp.fastq.gz
|
|
md5sum: 7a4ddf8485c147cd7aaf0d4f6cd57ace
|