Fix test syntax issues passing

workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4-tests.yml

@@ -35,8 +35,8 @@
     Database for Busco Lineage: v5
   outputs:
     Hifiasm HiC hap1:
-      assert: 
-        has_n_line:
+      asserts:
+        has_n_lines:
           n: 168
     Estimated Genome size: 2288021
     Busco Summary Hap1:
@@ -49,8 +49,8 @@
           value: 65000
           delta: 10000
     usable hap1 gfa:
-      assert: 
-        has_n_line:
+      asserts:
+        has_n_lines:
           n: 173
     Assembly statistics for Hap1 and Hap2:
       asserts:

workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0-tests.yml

@@ -25,6 +25,6 @@
           value: 68000
           delta: 5000
     mitogenome_genbank:
-      assert:
-        has_n_line:
+      asserts:
+        has_n_lines:
           n: 480

workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1-tests.yml

@@ -12,22 +12,18 @@
     Ploidy: 1
   outputs:
     GenomeScope linear plot:
-      class: File
       file: test-data/GenomeScope_Linear_plot.png
       compare: sim_size
       delta: 10000
     GenomeScope log plot:
-      class: File
       file: test-data/GenomeScope_Log_plot.png
       compare: sim_size
       delta: 10000
     GenomeScope transformed linear plot:
-      class: File
       file: test-data/GenomeScope_Transformed_linear_plot.png
       compare: sim_size
       delta: 10000
     GenomeScope transformed log plot:
-      class: File
       file: test-data/GenomeScope_Transformed_log_plot.png
       compare: sim_size
       delta: 10000

workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2-tests.yml

@@ -36,17 +36,14 @@
     Ploidy: 1
   outputs:
     GenomeScope linear plot (maternal):
-      class: File
       file: test-data/GenomeScope_Linear_plot_maternal.png
       compare: sim_size
       delta: 15000
     GenomeScope linear plot (paternal):
-      class: File
       file: test-data/GenomeScope_Linear_plot_paternal.png
       compare: sim_size
       delta: 15000
     GenomeScope linear plot (child):
-      class: File
       file: test-data/GenomeScope_Linear_plot_child.png
       compare: sim_size
       delta: 15000

workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection-tests.yml

@@ -5,55 +5,55 @@
       path: https://zenodo.org/records/11488310/files/shovill_contigs_fasta
   outputs:
     staramr_detailed_summary:
-        assert:
-        has_text:
-          text: "Resistance"
-        has_n_columns:
-          n: 12
+        asserts:
+          has_text:
+            text: "Resistance"
+          has_n_columns:
+            n: 12
     staramr_resfinder_report:
-        assert:
-        has_text:
-          text: "tetracycline"
-        has_n_columns:
-          n: 13
+        asserts:
+          has_text:
+            text: "tetracycline"
+          has_n_columns:
+            n: 13
     staramr_mlst_report:
-      assert:
+      asserts:
         has_text:
           text: "efaecalis"
         has_n_columns:
           n: 10
     staramr_plasmidfinder_report:
-      assert:
+      asserts:
         has_text:
           text: "CP002494"
         has_n_columns:
           n: 9
     staramr_summary:
-      assert:
+      asserts:
         has_text:
           text: "streptomycin"
         has_n_columns:
           n: 12
     amrfinderplus_report:
-      assert:
+      asserts:
         has_text:
           text: "Enterococcus faecalis quinolone resistant ParC"
         has_n_columns:
           n: 23
     amrfinderplus_mutation:
-      assert:
+      asserts:
         has_text:
           text: "cardiolipin synthase Cls"
         has_n_columns:
           n: 23
     abricate_virulence_report:
-      assert:
+      asserts:
         has_text:
           text: "endocarditis specific antigen"
         has_n_columns:
           n: 15
     tooldistillator_summarize:
-      assert:
+      asserts:
         has_text:
           text: "% Identity to reference sequence"
         has_text:

workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation-tests.yml

@@ -8,51 +8,51 @@
     Select a AMRFinderPlus database: amrfinderplus_V3.12_2024-05-02.2
   outputs:
     integronfinder2_logfile_text:
-      assert:
+      asserts:
         has_text:
           text: "Writing out results for replicon"
     integronfinder2_summary:
-      assert:
+      asserts:
         has_n_columns:
           n: 6
     integronfinder2_results_tabular:
-      assert:
+      asserts:
         has_n_columns:
           n: 14
     bakta_hypothetical_tabular:
-      assert:
+      asserts:
         has_n_columns:
           n: 9
     bakta_annotation_json:
-      assert:
+      asserts:
         has_text:
           text: "aa_hexdigest"
     bakta_annotation_tabular:
-      assert:
+      asserts:
         has_n_columns:
           n: 9
     isescan_results_tabular:
-      assert:
+      asserts:
         has_n_columns:
           n: 24
     isescan_summary_tabular:
-      assert:
+      asserts:
         has_text:
           text: "nIS"
     isescan_logfile_text:
-      assert:
+      asserts:
         has_text:
           text: "Both complete and partial IS elements are reported."
     plasmidfinder_result_json:
-      assert:
+      asserts:
         has_text:
           text: "positions_in_contig"
     plasmidfinder_results_tabular:
-      assert:
+      asserts:
         has_n_columns:
           n: 8
     tooldistillator_summarize:
-      assert:
+      asserts:
         has_text:
           text: "CDS12738(DOp1)"
         has_text:

workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring-tests.yml

@@ -21,10 +21,11 @@
     SuCOS threshold: 0
   outputs:
     Scored and filtered poses:
-      class: File
-      assert:
-        has_line: "$$$$"
-        n: 4
-      assert:
-        has_test: "SuCOS_Score"
-        n: 4
+      asserts:
+        has_line:
+          line: "$$$$"
+          n: 4
+      asserts:
+        has_text:
+          text: "SuCOS_Score"
+          n: 4

workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd-tests.yml

@@ -21,16 +21,19 @@
     XTC files:
       element_tests:
         split_file_000000.txt:
-          assert:
-            has_size: 138900
-            delta: 500
+          asserts:
+            has_size:
+              size: 138900
+              delta: 500
     Free energy data:
-      class: 'File'
-      assert:
-        has_n_lines: 101
-        has_n_columns: 5
+      asserts:
+        has_n_lines:
+          n: 101
+        has_n_columns:
+          n: 5
     Friction data:
-      class: 'File'
-      assert:
-        has_n_lines: 101
-        has_n_columns: 5
+      asserts:
+        has_n_lines:
+          n: 101
+        has_n_columns:
+          n: 5

workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa-tests.yml

@@ -15,18 +15,21 @@
     Salt concentration: 0.1
   outputs:
     MMGBSA free energy:
-      class: 'File'
-      assert:
-        has_n_lines: 2
+      asserts:
+        has_n_lines:
+          n: 2
     MMGBSA statistics:
       element_tests:
         split_file_000000.txt:
-          assert:
-            has_text: 'DELTA TOTAL'
-            has_text: 'Generalized Born ESURF calculated using LCPO'
+          asserts:
+          - that: has_text
+            text: 'DELTA TOTAL'
+          - that: has_text
+            text: 'Generalized Born ESURF calculated using LCPO'
     XTC files:
       element_tests:
         split_file_000000.txt:
-          assert:
-            has_size: 138900
-            delta: 500
+          asserts:
+            has_size:
+              size: 138900
+              delta: 500

workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates-tests.yml

@@ -23,8 +23,8 @@
     bin_size: 50
   outputs:
     average_bigwigs:
-      class: Collection
-      collection_type: list
+      attributes:
+        collection_type: list
       element_tests:
         ATAC_HH19_PT:
           asserts:

workflows/epigenetics/cutandrun/cutandrun-tests.yml

@@ -46,13 +46,15 @@
     MACS2 summits:
       element_tests:
         Rep1:
-          has_n_lines:
-            n: 1856
+          asserts:
+            has_n_lines:
+              n: 1856
     MACS2 narrowPeak:
       element_tests:
         Rep1:
-          has_n_lines:
-            n: 1856
+          asserts:
+            has_n_lines:
+              n: 1856
     MACS2 peaks xls:
       element_tests:
         Rep1:
@@ -109,13 +111,15 @@
     MACS2 summits:
       element_tests:
         Rep1:
-          has_n_lines:
-            n: 3261
+          asserts:
+            has_n_lines:
+              n: 3261
     MACS2 narrowPeak:
       element_tests:
         Rep1:
-          has_n_lines:
-            n: 3261
+          asserts:
+            has_n_lines:
+              n: 3261
     MACS2 peaks xls:
       element_tests:
         Rep1:

workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler-tests.yml

@@ -81,7 +81,6 @@
               value: 47830
               delta: 4000
     plot with pyGenomeTracks:
-      class: File
       file: test-data/plot_chic.png
       compare: sim_size
       delta: 1500

workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler-tests.yml

@@ -79,7 +79,6 @@
               value: 149349
               delta: 10000
     plot with pyGenomeTracks:
-      class: File
       file: test-data/plot_hic.png
       compare: sim_size
       delta: 1500