- 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.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 -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.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 -c ./tests/modules/fastp/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 -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.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

- 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: ce88539076ced5aff11f866836ea1f40
    - path: output/fastp/test_1.trim.fastq.gz
      md5sum: 65d75c13abbfbfd993914e1379634100
    - path: output/fastp/test_2.trim.fastq.gz
      md5sum: 0d87ce4d8ef29fb35f337eb0f6c9fcb4