Fix tests

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

@@ -33,8 +33,8 @@
     Name for Haplotype 2: Hap2
   outputs:
     Hifiasm HiC hap1:
-      assert: 
-        has_n_line:
+      asserts:
+        has_n_lines:
           n: 168
     Estimated Genome size: 2288021
     Busco Summary Hap1:
@@ -47,8 +47,8 @@
           value: 65000
           delta: 10000
     usable hap1 gfa:
-      assert: 
-        has_n_line:
+      asserts:
+        has_n_lines:
           n: 173
     Assembly statistics fir Hap1 and Hap2:
       asserts:

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

@@ -33,15 +33,15 @@
       delta: 10000
     GenomeScope summary:
       asserts:
-        has_text:
+        - has_text:
             text: '27,842 bp'
-        has_text:
+        - has_text:
             text: '35,913 bp'
     GenomeScope Model Parameters:
       asserts:
-        has_text:
+        - has_text:
             text: '0.0918418396430493'
-        has_text:
+        - has_text:
             text: '27.44263'
     Merged Meryl Database:
       asserts:

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

@@ -52,10 +52,10 @@
       delta: 15000
     GenomeScope summary (child):
       asserts:
-        has_text:
-          text: '39,419 bp'
-        has_text:
-          text: '43,763 bp'
+        - has_text:
+            text: '39,419 bp'
+        - has_text:
+            text: '43,763 bp'
     'Meryl database : Child':
       asserts:
         has_size:

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

@@ -22,9 +22,10 @@
   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
+        has_text:
+          text: "SuCOS_Score"
+          n: 4

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

@@ -21,16 +21,21 @@
     XTC files:
       element_tests:
         split_file_000000.txt:
-          assert:
-            has_size: 138900
-            delta: 500
+          asserts:
+            has_size:
+              value: 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

@@ -16,17 +16,21 @@
   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:
+            - has_text:
+                text: 'DELTA TOTAL'
+            - 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:
+              value: 138900
+              delta: 500

workflows/data-fetching/parallel-accession-download/parallel-accession-download-tests.yml

@@ -20,7 +20,7 @@
     Paired End Reads:
       element_tests:
         SRR11953971:
-          elements:
+          element_tests:
             forward:
               file: test-data/SRR11953971_1_head.fastq
               decompress: true

workflows/epigenetics/atacseq/atacseq-tests.yml

@@ -24,12 +24,12 @@
       element_tests:
         SRR891268_chr22_enriched:
           asserts:
-            - that: "has_text"
-              text: "32872 (11.70%) aligned concordantly 0 times"
-            - that: "has_text"
-              text: "108014 (38.44%) aligned concordantly exactly 1 time"
-            - that: "has_text"
-              text: "140078 (49.86%) aligned concordantly >1 times"
+            - has_text:
+                text: "32872 (11.70%) aligned concordantly 0 times"
+            - has_text:
+                text: "108014 (38.44%) aligned concordantly exactly 1 time"
+            - has_text:
+                text: "140078 (49.86%) aligned concordantly >1 times"
     MarkDuplicates metrics:
       element_tests:
         SRR891268_chr22_enriched:
@@ -60,10 +60,10 @@
       element_tests:
         SRR891268_chr22_enriched:
           asserts:
-            - that: "has_text"
-              text: "# tag size is determined as 47 bps"
-            - that: "has_text"
-              text: "# total tags in treatment: 234432"
+            - has_text:
+                text: "# tag size is determined as 47 bps"
+            - has_text:
+                text: "# total tags in treatment: 234432"
     Coverage from MACS2 (bigwig):
       element_tests:
         SRR891268_chr22_enriched:
@@ -125,9 +125,9 @@
               n: 4
     MultiQC webpage:
           asserts:
-            - that: "has_text"
-              text: "<a href=\"#cutadapt_filtered_reads\" class=\"nav-l2\">Filtered Reads</a>"
-            - that: "has_text"
-              text: "<td>% Aligned</td>"
-            - that: "has_text"
-              text: "<td>% BP Trimmed</td>"
+            - has_text:
+                text: "<a href=\"#cutadapt_filtered_reads\" class=\"nav-l2\">Filtered Reads</a>"
+            - has_text:
+                text: "<td>% Aligned</td>"
+            - has_text:
+                text: "<td>% BP Trimmed</td>"

workflows/epigenetics/chipseq-pe/chipseq-pe-tests.yml

@@ -24,12 +24,12 @@
   outputs:
     MultiQC webpage:
       asserts:
-        - that: "has_text"
-          text: "wt_H3K4me3"
-        - that: "has_text"
-          text: <a href="#cutadapt_filtered_reads" class="nav-l2">Filtered Reads</a>
-        - that: "has_text"
-          text: <a href="#bowtie2" class="nav-l1">Bowtie 2 / HiSAT2</a>
+        - has_text:
+            text: "wt_H3K4me3"
+        - has_text:
+            text: <a href="#cutadapt_filtered_reads" class="nav-l2">Filtered Reads</a>
+        - has_text:
+            text: <a href="#bowtie2" class="nav-l1">Bowtie 2 / HiSAT2</a>
     'MultiQC on input dataset(s): Stats':
       element_tests:
         bowtie2:
@@ -69,12 +69,12 @@
       element_tests:
         wt_H3K4me3:
           asserts:
-            - that: "has_text"
-              text: "# effective genome size = 1.87e+09"
-            - that: "has_text"
-              text: "# fragment size is determined as 201 bps"
-            - that: "has_text"
-              text: "# fragments after filtering in treatment: 41787"
+            - has_text:
+                text: "# effective genome size = 1.87e+09"
+            - has_text:
+                text: "# fragment size is determined as 201 bps"
+            - has_text:
+                text: "# fragments after filtering in treatment: 41787"
     MACS2 narrowPeak:
       element_tests:
         wt_H3K4me3:
@@ -85,12 +85,12 @@
       element_tests:
         wt_H3K4me3:
           asserts:
-            - that: "has_text"
-              text: "# effective genome size = 1.87e+09"
-            - that: "has_text"
-              text: "# fragment size is determined as 201 bps"
-            - that: "has_text"
-              text: "# fragments after filtering in treatment: 41787"
+            - has_text:
+                text: "# effective genome size = 1.87e+09"
+            - has_text:
+                text: "# fragment size is determined as 201 bps"
+            - has_text:
+                text: "# fragments after filtering in treatment: 41787"
     coverage from MACS2:
       element_tests:
         wt_H3K4me3:
@@ -102,9 +102,9 @@
       element_tests:
         wt_H3K4me3:
             asserts:
-            - that: "has_text"
-              text: "1622 (3.50%) aligned concordantly 0 times"
-            - that: "has_text"
-              text: "39144 (84.53%) aligned concordantly exactly 1 time"
-            - that: "has_text"
-              text: "5541 (11.97%) aligned concordantly >1 times"
+            - has_text:
+                text: "1622 (3.50%) aligned concordantly 0 times"
+            - has_text:
+                text: "39144 (84.53%) aligned concordantly exactly 1 time"
+            - has_text:
+                text: "5541 (11.97%) aligned concordantly >1 times"

workflows/epigenetics/chipseq-sr/chipseq-sr-tests.yml

@@ -15,12 +15,12 @@
   outputs:
     MultiQC webpage:
       asserts:
-        - that: "has_text"
-          text: "wt_H3K4me3"
-        - that: "has_text"
-          text: <a href="#cutadapt_filtered_reads" class="nav-l2">Filtered Reads</a>
-        - that: "has_text"
-          text: <a href="#bowtie2" class="nav-l1">Bowtie 2 / HiSAT2</a>
+        - has_text:
+            text: "wt_H3K4me3"
+        - has_text:
+            text: <a href="#cutadapt_filtered_reads" class="nav-l2">Filtered Reads</a>
+        - has_text:
+            text: <a href="#bowtie2" class="nav-l1">Bowtie 2 / HiSAT2</a>
     'MultiQC on input dataset(s): Stats':
       element_tests:
         bowtie2:
@@ -60,12 +60,12 @@
       element_tests:
         wt_H3K4me3:
           asserts:
-            - that: "has_text"
-              text: "# effective genome size = 1.87e+09"
-            - that: "has_text"
-              text: "# d = 200"
-            - that: "has_text"
-              text: "# tags after filtering in treatment: 44034"
+            - has_text:
+                text: "# effective genome size = 1.87e+09"
+            - has_text:
+                text: "# d = 200"
+            - has_text:
+                text: "# tags after filtering in treatment: 44034"
     MACS2 narrowPeak:
       element_tests:
         wt_H3K4me3:
@@ -76,12 +76,12 @@
       element_tests:
         wt_H3K4me3:
           asserts:
-            - that: "has_text"
-              text: "# effective genome size = 1.87e+09"
-            - that: "has_text"
-              text: "# d = 200"
-            - that: "has_text"
-              text: "# tags after filtering in treatment: 44034"
+            - has_text:
+                text: "# effective genome size = 1.87e+09"
+            - has_text:
+                text: "# d = 200"
+            - has_text:
+                text: "# tags after filtering in treatment: 44034"
     coverage from MACS2:
       element_tests:
         wt_H3K4me3:
@@ -93,9 +93,9 @@
       element_tests:
         wt_H3K4me3:
             asserts:
-            - that: "has_text"
-              text: "49251 reads; of these:"
-            - that: "has_text"
-              text: "43506 (88.34%) aligned exactly 1 time"
-            - that: "has_text"
-              text: "98.38% overall alignment rate"
+            - has_text:
+                text: "49251 reads; of these:"
+            - has_text:
+                text: "43506 (88.34%) aligned exactly 1 time"
+            - has_text:
+                text: "98.38% overall alignment rate"

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: