From e8bd730164f01b9409a87968ed54c55ad40b7fd0 Mon Sep 17 00:00:00 2001
From: kevinmenden <kevin.menden@t-online.de>
Date: Fri, 29 Jan 2021 16:14:33 +0100
Subject: [PATCH] added quast tests

---
 tests/software/quast/test.yml | 114 ++++++++++++++++++++++++++++++++++
 1 file changed, 114 insertions(+)

diff --git a/tests/software/quast/test.yml b/tests/software/quast/test.yml
index e69de29b..6d895298 100644
--- a/tests/software/quast/test.yml
+++ b/tests/software/quast/test.yml
@@ -0,0 +1,114 @@
+- name: quast_ref
+  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_ref -c ./tests/config/nextflow.config
+  tags:
+    - quast
+    - quast_reference
+  files:
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tsv
+      md5sum: 4d24cc0da823a100a076aef36f9fd75e
+    - path: ./output/quast/quast/contigs_reports/GCA_011545545_1_ASM1154554v1_cds_from_genomic.mis_contigs.fa
+    - path: ./output/quast/quast/contigs_reports/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.stdout
+    - path: ./output/quast/quast/aligned_stats/NGAx_plot.pdf
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tex
+      md5sum: ffe19cf4d5332952f0627e9cd82e3375
+    - path: ./output/quast/quast/aligned_stats/NAx_plot.pdf
+    - path: ./output/quast/quast/icarus.html
+    - path: ./output/quast/quast/report.tsv
+      md5sum: 503ebb57ffed0422fd7aff4025e21143
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.tex
+      md5sum: 85614257e0bb62ac750f7872886b2fbf
+    - path: ./output/quast/quast/basic_stats/gc.icarus.txt
+      md5sum: b3a770802ff9b2dd4ee8e47bddb2df3e
+    - path: ./output/quast/quast/aligned_stats/cumulative_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/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords
+      md5sum: dda3fc0addc41ecc0d5183dee6f95886
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.coords_tmp
+      md5sum: ce66eaeb99fdc11e4d50efadc1816e04
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tsv
+      md5sum: 769f2d9d7deb5e7a63e238d8ba0cfe13
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - 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/contigs_report_GCA_011545545-1_ASM1154554v1_cds_from_genomic.unaligned.info
+      md5sum: a8505cf206bf53ca369f7e3073fee587
+    - path: ./output/quast/quast/contigs_reports/minimap_output/GCA_011545545-1_ASM1154554v1_cds_from_genomic.sf
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 389e9fa2b29b967cb658c0770c941ce6
+    - path: ./output/quast/quast/genome_stats/GCA_011545545-1_ASM1154554v1_cds_from_genomic_gaps.txt
+      md5sum: c52381f09ea40b6141be5232494727b6
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/report.tsv
+      md5sum: 503ebb57ffed0422fd7aff4025e21143
+    - path: ./output/quast/quast/contigs_reports/transposed_report_misassemblies.txt
+      md5sum: 53c481fe8b3ef18280ea86cbded78b31
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.txt
+      md5sum: c1c26797084ea743ec5a224ab97adb1f
+    - path: ./output/quast/quast/report.txt
+      md5sum: 41bf3c24e68afce5ef0ba91004e57f7d
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: 2a69aada90cc1e788a4bc877c44d79c8
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_cds_from_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/contigs_reports/misassemblies_report.tsv
+      md5sum: 33144f8d064782864e8400e3a08b2a3a
+    - path: ./output/quast/quast/contigs_reports/unaligned_report.tex
+      md5sum: 48562e30903fcf33946e13b602b0e324
+    - path: ./output/quast/quast/contigs_reports/misassemblies_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: baab35c91e87432432113db1e4085f7b
+    - path: ./output/quast/quast/report.tex
+      md5sum: 8e72428ff7e7175bf47d58c10d8332e8
+    - path: ./output/quast/quast/contigs_reports/misassemblies_frcurve_plot.pdf
+    - 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/misassemblies_report.txt
+      md5sum: 0784e0d31e9f2a165730cc0029023427
+    - path: ./output/quast/quast/icarus_viewers/alignment_viewer.html
+      md5sum: bd63165a204a2ab424f8e81c647038d1
+    - path: ./output/quast/quast/contigs_reports/all_alignments_GCA_011545545-1_ASM1154554v1_cds_from_genomic.tsv
+      md5sum: c247152eb82b361106492642fd796e2c
+    - path: ./output/quast/quast/genome_stats/genome_info.txt
+      md5sum: 7c622ab66040d413a229419bf6b5181f
+    - path: ./output/quast/quast/basic_stats/NGx_plot.pdf
+    - 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.stderr
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
+      md5sum: c42838b1553759fb0460a9854e39da36
+    - path: ./output/quast/quast/report.html
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+
+- name: quast_noref
+  command: nextflow run ./tests/software/quast -profile docker -entry test_quast_noref -c ./tests/config/nextflow.config
+  tags:
+    - quast
+    - quast_no_reference
+  files:
+    - path: ./output/quast/quast/report.pdf
+    - path: ./output/quast/quast/basic_stats/GC_content_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tsv
+      md5sum: 1a82adfc057b6dc788034a6ce023cb56
+    - path: ./output/quast/quast/basic_stats/Nx_plot.pdf
+    - path: ./output/quast/quast/quast.log
+    - path: ./output/quast/quast/basic_stats/cumulative_plot.pdf
+    - path: ./output/quast/quast/transposed_report.tex
+      md5sum: a86aa094f9ab4bc1df35c5a7add2d0b0
+    - path: ./output/quast/quast/basic_stats/GCA_011545545.1_ASM1154554v1_genomic_GC_content_plot.pdf
+    - path: ./output/quast/quast/report.txt
+      md5sum: 7a2e442c18dd2730cfd38723f1c9c8f9
+    - path: ./output/quast/quast/icarus_viewers/contig_size_viewer.html
+      md5sum: dcf600c49ee86783475cb25215072630
+    - path: ./output/quast/quast/report.tsv
+      md5sum: 75882c0a5d811246395f5ea56146ce76
+    - path: ./output/quast/quast/report.tex
+      md5sum: 132edd2e916fc2a76a7b13973a0ffa4b
+    - path: ./output/quast/quast/icarus.html
+      md5sum: 9d7429362288c5078e6d6e7efcfc1ff7
+    - path: ./output/quast/quast/transposed_report.txt
+      md5sum: 154d88ec197c7b1bda5938232a79a00a
+    - path: ./output/quast/report.tsv
+      md5sum: 75882c0a5d811246395f5ea56146ce76
+    - path: ./output/quast/quast/report.html