update tests

Author: rpetit3

subworkflows/local/ariba/test.yml

@@ -14,9 +14,9 @@
     - path: bactopia-tools/ariba/ariba/SRR2838702/card/debug.report.tsv
       contains: ["ariba_ref_name", "reads", "resistance", "Clostridioides"]
     - path: bactopia-tools/ariba/ariba/SRR2838702/card/log.clusters.gz
-    - path: bactopia-tools/ariba/ariba/SRR2838702/card/report.tsv
+    - path: bactopia-tools/ariba/ariba/SRR2838702/card/SRR2838702-report.tsv
       contains: ["ariba_ref_name", "reads", "resistance", "Clostridioides"]
-    - path: bactopia-tools/ariba/ariba/SRR2838702/card/summary.csv
+    - path: bactopia-tools/ariba/ariba/SRR2838702/card/SRR2838702-summary.csv
       contains: ["name", "novel_var", "Clostridioides", "Neisseria"]
     - path: bactopia-tools/ariba/ariba/SRR2838702/card/version_info.txt
       contains: ["ARIBA", "Python", "OK", "True"]

subworkflows/local/iqtree/test.yml

@@ -39,8 +39,7 @@
     - path: bactopia-tools/iqtree/iqtree/test.iqtree
       contains: ['REFERENCES', 'GCF_000292685', 'Total']
     - path: bactopia-tools/iqtree/iqtree/test.mldist
-      md5sum: 8911a67ed8e329837f6673d9ad422c89
-    - path: bactopia-tools/iqtree/iqtree/test.model.gz
+      contains: ['GCF_000292685', 'GCF_002849995', 'GCF_000300075']
     - path: bactopia-tools/iqtree/iqtree/test.splits.nex
       md5sum: a257e91b7d51e5ce30e9c052428ce147
     - path: bactopia-tools/iqtree/iqtree/test.treefile

subworkflows/local/pangenome/test.yml

@@ -41,7 +41,6 @@
       contains: ['GCF_00029838', 'GCF_002849995']
     - path: bactopia-tools/pangenome/pangenome/iqtree/core-genome.mldist
       contains: ['GCF_00029838', 'GCF_002849995']
-    - path: bactopia-tools/pangenome/pangenome/iqtree/core-genome.model.gz
     - path: bactopia-tools/pangenome/pangenome/iqtree/core-genome.splits.nex
       md5sum: a257e91b7d51e5ce30e9c052428ce147
     - path: bactopia-tools/pangenome/pangenome/iqtree/core-genome.treefile

subworkflows/local/plasmidfinder/test.yml

@@ -13,7 +13,7 @@
     - path: bactopia-tools/plasmidfinder/plasmidfinder/GCF_000017085/GCF_000017085.tsv
       md5sum: 7aa17dc82d1efd058422d8e0cc45db1a
     - path: bactopia-tools/plasmidfinder/plasmidfinder/GCF_000017085/GCF_000017085.txt
-      md5sum: a86b2cb727f20a486edf852543d8c53b
+      contains: ['Results', 'Plasmid', 'Query', 'template']
     - path: bactopia-tools/plasmidfinder/plasmidfinder/GCF_000017085/logs/plasmidfinder/nf-plasmidfinder.begin
     - path: bactopia-tools/plasmidfinder/plasmidfinder/GCF_000017085/logs/plasmidfinder/nf-plasmidfinder.err
     - path: bactopia-tools/plasmidfinder/plasmidfinder/GCF_000017085/logs/plasmidfinder/nf-plasmidfinder.log

subworkflows/local/rgi/test.yml

@@ -21,7 +21,7 @@
     - path: bactopia-tools/rgi/rgi/GCA_000027305/logs/rgi/nf-rgi.trace
       contains: ['nextflow.trace']
     - path: bactopia-tools/rgi/rgi/GCA_000027305/logs/rgi/versions.yml
-      md5sum: 702fb41519f72203ddd2c9e2a38e9170
+      md5sum: 6edb5e8b85a3ea8e8a0961f1bfcaf3be
     - path: bactopia-tools/rgi/rgi/GCF_900478275/GCF_900478275.json
       contains: ["type_match", "model_name", "orf_dna_sequence"]
     - path: bactopia-tools/rgi/rgi/GCF_900478275/GCF_900478275.txt
@@ -39,7 +39,7 @@
     - path: bactopia-tools/rgi/rgi/GCF_900478275/logs/rgi/nf-rgi.trace
       contains: ['nextflow.trace']
     - path: bactopia-tools/rgi/rgi/GCF_900478275/logs/rgi/versions.yml
-      md5sum: 702fb41519f72203ddd2c9e2a38e9170
+      md5sum: 6edb5e8b85a3ea8e8a0961f1bfcaf3be
     - path: bactopia-tools/rgi/rgi/logs/csvtk_concat/nf-csvtk_concat.begin
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: bactopia-tools/rgi/rgi/logs/csvtk_concat/nf-csvtk_concat.err

subworkflows/local/snippy/test.yml

@@ -76,9 +76,9 @@
     - path: bactopia-tools/snippy/snippy/logs/snippy-core/nf-snippy-core.begin
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: bactopia-tools/snippy/snippy/logs/snippy-core/nf-snippy-core.err
-      md5sum: 465702fe9eeb4ba97a6a6e86d84b8975
+      contains: ['test', 'core-snp', 'Done', 'snippy-core']
     - path: bactopia-tools/snippy/snippy/logs/snippy-core/nf-snippy-core.log
-      md5sum: 465702fe9eeb4ba97a6a6e86d84b8975
+      contains: ['test', 'core-snp', 'Done', 'snippy-core']
     - path: bactopia-tools/snippy/snippy/logs/snippy-core/nf-snippy-core.out
       md5sum: d41d8cd98f00b204e9800998ecf8427e
     - path: bactopia-tools/snippy/snippy/logs/snippy-core/nf-snippy-core.run