- name: quast_ref
  command: nextflow run ./tests/software/quast -entry test_quast_ref -c ./tests/config/nextflow.config
  tags:
    - quast
    - quast_reference
  files:
    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords.filtered
      md5sum: ec9191d0acb5d5bce56b4842551a8598
    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
      md5sum: c42838b1553759fb0460a9854e39da36
    - path: ./output/quast/report.tsv
      md5sum: b203a9d2c995bd66552eeb5cb0a98762
    - path: ./output/quast/quast/report.tex
      md5sum: 8168f197dfb2f781accdefaa0d90fc87
    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
    - path: ./output/quast/quast/transposed_report.tex
      md5sum: 0b8fd00649a5758024c8093d5919f71c
    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords
      md5sum: dda3fc0addc41ecc0d5183dee6f95886
    - path: ./output/quast/quast/transposed_report.txt
      md5sum: 73216314e65ef91c24422d5bdd0795e4
    - path: ./output/quast/quast/report.html
    - path: ./output/quast/quast/report.pdf
    - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv
      md5sum: c247152eb82b361106492642fd796e2c
    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.used_snps.gz
      md5sum: 7b1db1b433cd95243a949bcb72e7e3a6
    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
      md5sum: 48562e30903fcf33946e13b602b0e324
    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
      md5sum: 53c481fe8b3ef18280ea86cbded78b31
    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.mis_contigs.info
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
      md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13
    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
    - path: ./output/quast/quast/genome_stats/features_cumulative_plot.pdf
    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
      md5sum: 85614257e0bb62ac750f7872886b2fbf
    - path: ./output/quast/quast/quast.log
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
      md5sum: 33144f8d064782864e8400e3a08b2a3a
    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info
      md5sum: a8505cf206bf53ca369f7e3073fee587
    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_genomic_features_any.txt
      md5sum: 307b3bb1f42fc2f11a60a2e9846021d7
    - path: ./output/quast/quast/icarus.html
      md5sum: 6e57f5f7d07528496fc2f35b449951fe
    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
      md5sum: 4d24cc0da823a100a076aef36f9fd75e
    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stderr
    - path: ./output/quast/quast/aligned_stats/cumulative_plot.pdf
    - path: ./output/quast/quast/genome_stats/genome_info.txt
      md5sum: bc3df27ad7356c045c9a108f9d4bcfbe
    - path: ./output/quast/quast/genome_stats/features_frcurve_plot.pdf
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.txt
      md5sum: 0784e0d31e9f2a165730cc0029023427
    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout
    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
      md5sum: c1c26797084ea743ec5a224ab97adb1f
    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt
      md5sum: c52381f09ea40b6141be5232494727b6
    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
      md5sum: ad5176f21d3c4809a9a8f9c27bb8d70a
    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
      md5sum: ffe19cf4d5332952f0627e9cd82e3375
    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp
      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
    - path: ./output/quast/quast/transposed_report.tsv
      md5sum: 1754bd6c6fa8a0172a342a48dd3ca505
    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
    - path: ./output/quast/quast/report.txt
      md5sum: e334b3390a5028cbf88fe4ccab2b6499
    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
    - path: ./output/quast/quast/report.tsv
      md5sum: b203a9d2c995bd66552eeb5cb0a98762
    - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa
      md5sum: d41d8cd98f00b204e9800998ecf8427e
    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf

- name: quast_noref
  command: nextflow run ./tests/software/quast -entry test_quast_noref -c ./tests/config/nextflow.config
  tags:
    - quast
    - quast_no_reference
  files:
    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
      md5sum: d2680b8083139e62baf7af0f852d52b8
    - path: ./output/quast/quast/transposed_report.txt
      md5sum: b6b126e9dcfd8c8e7bd36dff9220caf0
    - path: ./output/quast/report.tsv
      md5sum: 55d2938fcdb678e97d441cf32b9c740e
    - path: ./output/quast/quast/icarus.html
      md5sum: dcb11b4c7b6c21190c1344c46288d3f4
    - path: ./output/quast/quast/report.txt
      md5sum: c8e87f40e888a0395be04f78532d9deb
    - path: ./output/quast/quast/transposed_report.tsv
      md5sum: 27b6c755be5d70e3eed22e1bf3f68ce5
    - path: ./output/quast/quast/quast.log
    - path: ./output/quast/quast/report.tex
      md5sum: 69c31172ae6257663b22bb192ba84682
    - path: ./output/quast/quast/report.pdf
    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
    - path: ./output/quast/quast/report.tsv
      md5sum: 55d2938fcdb678e97d441cf32b9c740e
    - path: ./output/quast/quast/transposed_report.tex
      md5sum: 213fb615afe21904e52d670e602c1f62
    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
    - path: ./output/quast/quast/report.html