- 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: 2616b6791fd89fb1cc2d16a73b9463b0
    - 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: 25ec85e3534f380ca2109c894671f1ed
    - 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: 7e10b0b12fab5cff620fdeb1a32392f8
    - 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"