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nf-core_modules/tests/modules/fastp/test.yml
Adam Talbot 7e8ad56688
module FASTP: Support for interleaved FASTQ (#1891) 
* 1882 FASTP now supports interleaved FASTQ files

Changes:
 - single_end FASTP pipes the FASTQ file
 - Using args, it can be configured for interleaved in `--interleaved_in`
 - Out is automatically interleaved if input is paired end.
 - Removed md5sum checks for FASTQ files as compression seemed to cause
 differences
 - Instead, we check inside the FASTQ files for content.

Relates to #1882

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
2022-07-19 16:27:15 +01:00

191 lines
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- 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
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"
- 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: 803a024342be986f76486f6ffea15909
- 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
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"
- path: output/fastp/test_2.fastp.fastq.gz
contains:
- "@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"
- name: fastp test_fastp_interleaved
command: nextflow run ./tests/modules/fastp -entry test_fastp_interleaved -c ./tests/config/nextflow.config -c ./tests/modules/fastp/nextflow.config
tags:
- fastp
files:
- path: output/fastp/test.fastp.fastq.gz
contains:
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/1"
- "TCATAAACCAAAGCACTCACAGTGTCAACAATTTCAGCAGGACAACGCCGACAAGTTCCGAGGAACATGTCTGGACCTATAGTTTTCATAAGTCTACACACTGAATTGAAATATTCTGGTTCTAGTGTGCCCTTAGTTAGCAATGTGCGT"
- "AAAAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEE<EEAAAEEEEEEEEEAAAAEAEEEAEEEEEE<AAAA"
- "@ERR5069949.2151832 NS500628:121:HK3MMAFX2:2:21208:10793:15304/2"
- "ATGTGTACATTGGCGACCCTGCTCAATTACCTGCACCACGCACATTGCTAACTAAGGGCACACTAGAACCAGAATATTTCAATTCAGTGTGTAGACTTATGAAAACTATAGGTCCAGACATGTTCCTCGGAACTTGTCGGCGTTGTCCTG"
- "AAAAAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAEEEEEEEEEE/EEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEAAEEEEEEEAEEEEEAAEEEEEEEEEAAEAAA<<EAAEEEEEEEAAA<<<AE"
- path: output/fastp/test.fastp.html
contains:
- "Q20 bases:</td><td class='col2'>25.719000 K (93.033098%)"
- "paired end (151 cycles + 151 cycles)"
- path: output/fastp/test.fastp.json
md5sum: 5b70f43f33778d278a84b3e9270fa114
- path: output/fastp/test.fastp.log
contains:
- "Q20 bases: 12922(92.9841%)"
- "reads passed filter: 198"
- 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
contains:
- "@ERR5069949.885966 NS500628:121:HK3MMAFX2:4:11610:19682:20132/1 failed_quality_filter"
- "GTCTAATCATAATTTCTTGGTACAGGCTGGTATTGTTCATCTCAGGGTTATTGGACATTCTATGCAAAATTGTGTACTT"
- "AAA//E/EAA/E//E//E//E/E//AE/A/E//EAEA///AE//E///E/EEE6EEEAEEA///E/AEE/EAEE/E//E"
- path: output/fastp/test.fastp.fastq.gz
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"
- 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: b647fa752d3fe7956d17429bfe27d72c
- 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.fastp.fastq.gz
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"
- path: output/fastp/test_2.fastp.fastq.gz
contains:
- "@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
- path: output/fastp/test_2.fail.fastq.gz
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"
- 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_1.fastp.fastq.gz
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"
- path: output/fastp/test_2.fastp.fastq.gz
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"
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