- name: quast with reference
  command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
  tags:
    - quast
    - quast_reference
  files:
    - path: ./output/quast/report.tsv
    - path: ./output/quast/quast/transposed_report.txt
      md5sum: 73ae4f7cbe0da640819214cb013a79ef
    - path: ./output/quast/quast/transposed_report.tex
      md5sum: 117ed0d235b8e74b8f7ae8ed7b78c449
    - path: ./output/quast/quast/icarus.html
    - path: ./output/quast/quast/transposed_report.tsv
      md5sum: 475bf9987c421b72fe1675b54ae0bcbe
    - path: ./output/quast/quast/report.tex
      md5sum: e4c1d12bfe94d5a10e2264397bb90f83
    - path: ./output/quast/quast/report.txt
      md5sum: 6295e6d462b1db45b1bb9f3f508275ad
    - path: ./output/quast/quast/report.tsv
      md5sum: b70404d2b4d4e905afcfe3d149a5bd15
    - path: ./output/quast/quast/report.html
    - path: ./output/quast/quast/report.pdf
    - path: ./output/quast/quast/quast.log
    - path: ./output/quast/quast/genome_stats/test_transcriptome_genomic_features_any.txt
      md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
    - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
    - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
    - path: ./output/quast/quast/genome_stats/genome_info.txt
      md5sum: a4bb1f2792c175fc8d7fbf37f219e552
    - path: ./output/quast/quast/genome_stats/test_transcriptome_gaps.txt
      md5sum: c52381f09ea40b6141be5232494727b6
    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
    - path: ./output/quast/quast/basic_stats/test_transcriptome_GC_content_plot.pdf
    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.mis_contigs.info
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.unaligned.info
      md5sum: a8505cf206bf53ca369f7e3073fee587
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
      md5sum: 4895cb02a010f1db85fc4992ac3c63b1
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
      md5sum: d5c9dd22ce8f382649f74ba1f61d8a84
    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stdout
    - path: ./output/quast/quast/contigs_reports/all_alignments_test_transcriptome.tsv
      md5sum: c247152eb82b361106492642fd796e2c
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
      md5sum: 0df52940978f10c0fc9ed5f6770f170e
    - path: ./output/quast/quast/contigs_reports/test_transcriptome.mis_contigs.fa
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
      md5sum: d83abdf60e7ef02354a783dff4262d7d
    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
      md5sum: f2adf811a611abdcb9f10bd7801e61e1
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
      md5sum: dd6e08408ea9a6830d47d5c21b84d587
    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
      md5sum: e77d87bafe0e2c881805f8dfcc5f2351
    - path: ./output/quast/quast/contigs_reports/contigs_report_test_transcriptome.stderr
    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
      md5sum: 6f9bd38e646b0a754b153e0dfe2c57b0
    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords.filtered
      md5sum: ec9191d0acb5d5bce56b4842551a8598
    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords
      md5sum: dda3fc0addc41ecc0d5183dee6f95886
    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.used_snps.gz
      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.sf
    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.unaligned
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/minimap_output/test_transcriptome.coords_tmp
      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html

- name: quast without reference
  command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
  tags:
    - quast
    - quast_no_reference
  files:
    - path: ./output/quast/report.tsv
      md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
    - path: ./output/quast/quast/transposed_report.txt
      md5sum: 5496230d4bc3846616d7e08d52ffc081
    - path: ./output/quast/quast/transposed_report.tex
      md5sum: cf6a3b50575b510a7c42f5e745dd8674
    - path: ./output/quast/quast/icarus.html
      md5sum: ba0ddcdbcd743191d282e3986cb68735
    - path: ./output/quast/quast/transposed_report.tsv
      md5sum: 4b128bbf595b07dd2e2d5230bf575d29
    - path: ./output/quast/quast/report.tex
      md5sum: ac22b93fad7cdb6a812e5f670e815647
    - path: ./output/quast/quast/report.txt
      md5sum: 283160faa1d8cd32064c49e3c6d738d5
    - path: ./output/quast/quast/report.tsv
      md5sum: 94e7fd30b8147f1b9df4373ad865c0aa
    - path: ./output/quast/quast/report.html
    - path: ./output/quast/quast/report.pdf
    - path: ./output/quast/quast/quast.log
    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
    - path: ./output/quast/quast/basic_stats/test_genome_GC_content_plot.pdf
    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html