- name: quast with reference
  command: nextflow run ./tests/modules/quast -entry test_quast_ref -c ./tests/config/nextflow.config
  tags:
    - quast
  files:
    - path: ./output/quast/report.tsv
    - path: ./output/quast/quast/transposed_report.txt
      md5sum: 5dee51af1e7f916200d0a80f0c66be60
    - path: ./output/quast/quast/transposed_report.tex
      md5sum: 336ec8d7b403fe1e0519e3a39eadd691
    - path: ./output/quast/quast/icarus.html
    - path: ./output/quast/quast/transposed_report.tsv
      md5sum: 0e1b2eff1e8fd91a0bf80165d8f31ae5
    - path: ./output/quast/quast/report.tex
      md5sum: a9aac7d2ac2263df7e4599e4431c7393
    - path: ./output/quast/quast/report.txt
      md5sum: 2da78350f20819f2625bd467800700ad
    - path: ./output/quast/quast/report.tsv
      md5sum: 38fb41afadc09ffcbef62e42fea49f5e
    - path: ./output/quast/quast/report.html
    - path: ./output/quast/quast/report.pdf
    - path: ./output/quast/quast/quast.log
    - path: ./output/quast/quast/genome_stats/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: d0193b322079565dc78608291e9c44d1
    - path: ./output/quast/quast/genome_stats/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/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_transcriptome.mis_contigs.info
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.unaligned.info
      md5sum: a8505cf206bf53ca369f7e3073fee587
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
      md5sum: d778f337899736cc62ed837b739b375c
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
      md5sum: 8b9a6d675a41bab6bf344dde2a20a939
    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stdout
    - path: ./output/quast/quast/contigs_reports/all_alignments_transcriptome.tsv
      md5sum: c247152eb82b361106492642fd796e2c
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
      md5sum: ec1f7a1d1fb4a1b465057cf897b90b51
    - path: ./output/quast/quast/contigs_reports/transcriptome.mis_contigs.fa
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
      md5sum: fdb440c653e2f0306286798cacceaadb
    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
      md5sum: 81d9597314356363a6b4e0d67027345a
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
      md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3
    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
      md5sum: a32a09a0df811d1a75fbfe124081d1ca
    - path: ./output/quast/quast/contigs_reports/contigs_report_transcriptome.stderr
    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
      md5sum: e8e3bcb86da2cbd8eded980de80fa45c
    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords.filtered
      md5sum: ec9191d0acb5d5bce56b4842551a8598
    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.coords
      md5sum: dda3fc0addc41ecc0d5183dee6f95886
    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.used_snps.gz
      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.sf
    - path: ./output/quast/quast/contigs_reports/minimap_output/transcriptome.unaligned
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/minimap_output/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/modules/quast -entry test_quast_noref -c ./tests/config/nextflow.config
  tags:
    - quast
  files:
    - path: ./output/quast/report.tsv
      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
    - path: ./output/quast/quast/transposed_report.txt
      md5sum: 8784d7c7349498e1507e09fbf554625d
    - path: ./output/quast/quast/transposed_report.tex
      md5sum: 4c2a9dd0c1d3cbb80a2ac2577b5d363b
    - path: ./output/quast/quast/icarus.html
      md5sum: ecc0b67f3d4ff54568dfb83d8ac5911b
    - path: ./output/quast/quast/transposed_report.tsv
      md5sum: f0b5f65b2050af83b6d170d384c7616b
    - path: ./output/quast/quast/report.tex
      md5sum: 3da038cc5a02ef83e225c5277b87970b
    - path: ./output/quast/quast/report.txt
      md5sum: bd2faaef244f02aa072d544c0d6d6e71
    - path: ./output/quast/quast/report.tsv
      md5sum: 074e239aac0f298cf4cd2a28a9bb5690
    - 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/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