2021-03-24 16:08:59 +00:00
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|
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- name: fastp test_fastp_single_end
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2022-06-24 08:01:14 +00:00
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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2021-02-01 13:02:06 +00:00
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tags:
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2021-03-24 16:08:59 +00:00
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|
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- fastp
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2021-02-01 13:02:06 +00:00
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files:
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2022-06-24 08:01:14 +00:00
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- path: output/fastp/test.fastp.fastq.gz
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2022-07-19 15:27:15 +00:00
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contains:
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|
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
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- "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
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- "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
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|
|
- "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
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|
- "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
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|
|
|
- "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
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2021-03-24 16:08:59 +00:00
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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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2022-06-24 08:01:14 +00:00
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- path: output/fastp/test.fastp.json
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2022-07-19 15:27:15 +00:00
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md5sum: 803a024342be986f76486f6ffea15909
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2021-03-24 16:08:59 +00:00
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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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2021-02-01 13:02:06 +00:00
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2021-03-24 16:08:59 +00:00
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- name: fastp test_fastp_paired_end
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2022-06-24 08:01:14 +00:00
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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2021-02-01 13:02:06 +00:00
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tags:
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2021-03-24 16:08:59 +00:00
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- fastp
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2021-02-01 13:02:06 +00:00
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files:
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2021-03-24 16:08:59 +00:00
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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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2022-06-24 08:01:14 +00:00
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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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2021-03-24 16:08:59 +00:00
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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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2022-06-24 08:01:14 +00:00
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- path: output/fastp/test_1.fastp.fastq.gz
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2022-07-19 15:27:15 +00:00
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contains:
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|
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
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|
- "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
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|
- "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
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|
|
|
- "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
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|
|
|
- "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
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|
|
|
- "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
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2022-06-24 08:01:14 +00:00
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- path: output/fastp/test_2.fastp.fastq.gz
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2022-07-19 15:27:15 +00:00
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contains:
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- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
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- "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
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- "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
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|
|
- "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2"
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- "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT"
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- "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
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- name: fastp test_fastp_interleaved
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command: nextflow run ./tests/modules/fastp -entry test_fastp_interleaved -c ./tests/config/nextflow.config -c ./tests/modules/fastp/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.fastq.gz
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contains:
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- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
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- "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
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- "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
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|
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
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- "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
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- "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
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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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- "paired end (151 cycles + 151 cycles)"
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- path: output/fastp/test.fastp.json
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md5sum: 5b70f43f33778d278a84b3e9270fa114
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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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|
|
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- "reads passed filter: 198"
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2021-07-21 08:00:48 +00:00
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- name: fastp test_fastp_single_end_trim_fail
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2022-06-24 08:01:14 +00:00
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command: nextflow run ./tests/modules/fastp -entry test_fastp_single_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
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2021-07-21 08:00:48 +00:00
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tags:
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|
- fastp
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|
|
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files:
|
2022-06-24 08:01:14 +00:00
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|
|
- path: output/fastp/test.fail.fastq.gz
|
2022-07-19 15:27:15 +00:00
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contains:
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|
- "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/1 failed_quality_filter"
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- "GTCTAATCATAATTTCTTGGTACAGGCTGGTATTGTTCATCTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTT"
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- "AAA//E/EAA/E//E//E//E/E//AE/A/E//EAEA///AE//E///E/EEE6EEEAEEA///E/AEE/EAEE/E//E"
|
2022-06-24 08:01:14 +00:00
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- path: output/fastp/test.fastp.fastq.gz
|
2022-07-19 15:27:15 +00:00
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contains:
|
|
|
|
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
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|
|
|
- "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
|
|
|
|
- "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
|
|
|
|
- "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
|
|
|
|
- "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
|
|
|
|
- "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
|
2021-07-21 08:00:48 +00:00
|
|
|
- path: output/fastp/test.fastp.html
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|
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contains:
|
|
|
|
- "Q20 bases:</td><td class='col2'>12.922000 K (92.984097%)"
|
|
|
|
- "single end (151 cycles)"
|
2022-06-24 08:01:14 +00:00
|
|
|
- path: output/fastp/test.fastp.json
|
2022-07-19 15:27:15 +00:00
|
|
|
md5sum: b647fa752d3fe7956d17429bfe27d72c
|
2021-07-21 08:00:48 +00:00
|
|
|
- path: output/fastp/test.fastp.log
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|
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contains:
|
|
|
|
- "Q20 bases: 12922(92.9841%)"
|
|
|
|
- "reads passed filter: 99"
|
|
|
|
|
|
|
|
- name: fastp test_fastp_paired_end_trim_fail
|
2022-06-24 08:01:14 +00:00
|
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_trim_fail -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
|
2021-07-21 08:00:48 +00:00
|
|
|
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
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|
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contains:
|
|
|
|
- '"passed_filter_reads": 198'
|
2022-06-24 08:01:14 +00:00
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|
- path: output/fastp/test_1.fastp.fastq.gz
|
2022-07-19 15:27:15 +00:00
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contains:
|
|
|
|
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
|
|
|
|
- "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
|
|
|
|
- "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
|
|
|
|
- "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1"
|
|
|
|
- "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
|
|
|
|
- "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
|
2022-06-24 08:01:14 +00:00
|
|
|
- path: output/fastp/test_2.fastp.fastq.gz
|
2022-07-19 15:27:15 +00:00
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contains:
|
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|
|
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
|
|
|
|
- "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
|
|
|
|
- "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
|
|
|
|
- "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/2"
|
|
|
|
- "GCATAGACGGTGCTTTACTTACAAAGTCCTCAGAATACAAAGGTCCTATTACGGATGTTTTCTACAAAGAAAACAGT"
|
|
|
|
- "AAAAA6EEAEEEEEAEEAEEAEEEEEEA6EEEEAEEAEEEEE6EEEEEEAEEEEA///A<<EEEEEEEEEAEEEEEE"
|
|
|
|
- path: output/fastp/test_1.fail.fastq.gz
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|
- path: output/fastp/test_2.fail.fastq.gz
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contains:
|
|
|
|
- "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/2"
|
|
|
|
- "CTTAGGTCTTAGGATTGGCTGTATCAACCTTAAGCTTAAGTACACAATTTTGCATAGAATGTCCAATAA"
|
|
|
|
- "A//AA6EEAEEEEE6EEE/EEA/EA///AAE/EAEEEAE6AE/E/E/EEAAE/EAA/E/E/<EA//E/6"
|
2021-07-23 09:44:00 +00:00
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|
|
- name: fastp test_fastp_paired_end_merged
|
2022-06-24 08:01:14 +00:00
|
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command: nextflow run ./tests/modules/fastp -entry test_fastp_paired_end_merged -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
|
2021-07-23 09:44:00 +00:00
|
|
|
tags:
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|
|
|
- fastp
|
|
|
|
files:
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|
- path: output/fastp/test.fastp.html
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contains:
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|
- "<div id='After_filtering__merged__quality'>"
|
|
|
|
- path: output/fastp/test.fastp.json
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contains:
|
|
|
|
- '"merged_and_filtered": {'
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|
|
|
- '"total_reads": 75'
|
|
|
|
- '"total_bases": 13683'
|
|
|
|
- path: output/fastp/test.fastp.log
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contains:
|
|
|
|
- "Merged and filtered:"
|
|
|
|
- "total reads: 75"
|
|
|
|
- "total bases: 13683"
|
2022-06-24 08:01:14 +00:00
|
|
|
- path: output/fastp/test_1.fastp.fastq.gz
|
2022-07-19 15:27:15 +00:00
|
|
|
contains:
|
|
|
|
- "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/1"
|
|
|
|
- "CCTTATGACAGCAAGAACTGTGTATGATGATGGTGCTAGGAGAGTGTGGACACTTATGAATGTCTTGACACTCGTTTATAAAGTTTATTATGGTAATGCTTTAGATCAAGCCATTTCCATGTGGGCTCTTATAATCTCTGTTACTTC"
|
|
|
|
- "AAAAAEAEEAEEEEEEEEEEEEEEEEAEEEEAEEEEEEEEAEEEEEEEEEEEEEEEEE/EAEEEEEE/6EEEEEEEEEEAEEAEEE/EE/AEEAEEEEEAEEEA/EEAAEAE<AEEAEEEAEAEEEAEAEEAE/AEEEEAEEEEAEA"
|
|
|
|
- "@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/1"
|
|
|
|
- "CACAAACTCTAAAAGAATGTATAGGGTCAGCACCAAAAATACCAGCAGATAATAATGTTGCAAGTAGAACTTCGTGCAGATTAAAATTTTCATAAGCACTCTAAAGAAGTTGAATGTCTTCAAATTTCTTAACATTAGGGCCCACAACAAG"
|
|
|
|
- "AAAAAEA/A<EAA/AE/EE/EE//////EA/EEE/E/EEEE//E/6//EA//<AA/A/EEEAA/EEEE/EEEA/E/</AEE////AEEEE//<E//EAE/A///<EEE//<E<<EEE<///A//E/E/EEEAA/<A////<A/AEAAA//E"
|
2022-06-24 08:01:14 +00:00
|
|
|
- path: output/fastp/test_2.fastp.fastq.gz
|
2022-07-19 15:27:15 +00:00
|
|
|
contains:
|
|
|
|
- "@ERR5069949.1066259 NS500628:121:HK3MMAFX2:1:11312:18369:8333/2"
|
|
|
|
- "GTACAAAAATAGCCTAAGAAACAATAAACTAGCATTATACACTGAAGTGTATTACCAGTTATGAAGAAAATAGGGCAATACTCAACACACATAAAAACAATACCTCTGGCCAAAAACATGACAGTTGTAACTACACCTGAGTAGTTAGAAG"
|
|
|
|
- "AAAAAEEEEEEEEAEEEEEEEEEEEEEEEEEEEEEEEEAEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEA/EAA</EEEEEEEEEE/AE//A/E<AE<AA<AEEE/AAEAAAEEAEEA<A6AEEA<EEAEEEEEEEAA//EE"
|
|
|
|
- "@ERR5069949.324865 NS500628:121:HK3MMAFX2:1:11102:17526:14721/2"
|
|
|
|
- "ATGAATCTGATGAATACATAGCTACTAATGGACCTCTTAAAGTGCGTGGTAGTTGTGATTAAAGCGGACACATACTTGCTAAACACTCTCTTCATGATGTC"
|
|
|
|
- "A/AAAEEEEA6AA6EE//EEA/EEEAE/EA/A////E</EEAA//EEA////EAE<///E/AEA</AAE/EA//E<EAAAE/AA//AEE//A/AE//</EE"
|
|
|
|
- path: output/fastp/test.merged.fastq.gz
|
|
|
|
contains:
|
|
|
|
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1 merged_150_37"
|
|
|
|
- "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGTGGTGCAGGTAATTGAGCAGGGTCGCCAATGTACACAT"
|
|
|
|
- "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAAEEEEEEEEEEEEEEEEEEEEE/EEEEEEEEEEAAAAA"
|
|
|
|
- "@ERR5069949.576388 NS500628:121:HK3MMAFX2:4:11501:11167:14939/1 merged_77_0"
|
|
|
|
- "ACTGTTTTCTTTGTAGAAAACATCCGTAATAGGACCTTTGTATTCTGAGGACTTTGTAAGTAAAGCACCGTCTATGC"
|
|
|
|
- "AAA6AEEEEEEEEEAEEE/6EEAEEEAEEEEEAEEEEEEEEEEEEEEEEEEEEE<AAEEEEEEEEEEE</EEEA/AE"
|