finish and fix tests

workflows/amplicon/dada2/README.md

@@ -18,7 +18,7 @@ As a first step the input collection is sorted. This is important because the da
 a collection in sorted order. If the input collection would not be sorted then the mergePairs step
 samples would be mixed up.
 
-- `FilterAndTrim` Qualitycontrol by filtering and trimming reads
+- `FilterAndTrim` Quality control by filtering and trimming reads
 - `QualityProfile` is called before and after the FilterAndTrim step
 - `Unzip Collection` separates forward and reverse reads (the next steps are evaluated separately on forward and reverse reads)
 - `learnErrors` learn error rates
@@ -28,3 +28,12 @@ samples would be mixed up.
 - `removeBimeraDenovo` remove chimeric sequencs
 - `assignTaxonomy` assign taxonomic information from a reference data base
 
+## TODO
+
+Some possibilities to extend/improve the workflow
+
+- output BIOM
+- use ASV1, ... in sequence table and taxonomy output, and output additional fasta
+- allow to use custom taxonmoy / make it optional
+
+

workflows/amplicon/dada2/dada2_paired-tests.yml

@@ -57,12 +57,30 @@
     Read length forward read: '240'
     Read length reverse read: '160'
     Pool samples: 'FALSE'
-    Reference database: silva_138
+    Cached reference database: silva_138
   outputs:
     Sequence Table:
       path: test-data/Sequence Table.dada2_sequencetable
+      asserts:
+        - has_n_columns:
+            n: 6
+        - has_n_lines:
+            n: 171
     Counts:
       path: test-data/Counts.tabular
+      asserts:
+        - has_n_columns:
+            n: 8
+        - has_n_lines:
+            n: 6
     Taxonomy:
-      path: test-data/Taxonomy.tabular
+      ftype: tabular
       sorted: true
+      asserts:
+        - has_text:
+            text: Firmicutes
+            n: 136
+        - has_n_columns:
+            n: 7
+        - has_n_lines:
+            n: 171