Add Maker annotation workflow

workflows/genome-annotation/maker-annotation-eukaryote/.dockstore.yml

@@ -0,0 +1,7 @@
+version: 1.2
+workflows:
+- name: "main"
+  primaryDescriptorPath: /maker-annotation-eukaryote.ga
+  subclass: Galaxy
+  testParameterFiles:
+  - /maker-annotation-eukaryote-tests.yml

workflows/genome-annotation/maker-annotation-eukaryote/CHANGELOG.md

@@ -0,0 +1,7 @@
+# Changelog
+
+## [0.1] 2021-09-20
+
+### Added
+
+- Initial version of Annotation of eukaryotic genomes with MAKER workflow

workflows/genome-annotation/maker-annotation-eukaryote/README.md

@@ -0,0 +1,12 @@
+Annotation of eukaryotic genomes with MAKER
+-------------------------------------------
+
+This workflow describes the necessary steps to annotate eukaryotic genomes by using the MAKER tool. Its original version appears in the GTN under the title [Genome annotation with Maker](https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-maker/tutorial.html).
+
+### Workflow evaluation
+
+Comparing annotation workflows and deciding which one is the best is an open question. 
+
+As a possible approach to assess whether changes in the workflow contribute to its improvement, one possibility is to use the [ParseVal](https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/aegean_parseval/aegean_parseval/0.16.0) tool, in order to compare the obtained result with a standard annotation.
+
+If you only want to know is an annotation looks reasonable based on the current test data, you can just count the genes in the output GFF, and/or compare the total length of genes.

workflows/genome-annotation/maker-annotation-eukaryote/maker-annotation-eukaryote-tests.yml

@@ -0,0 +1,122 @@
+- doc: Test outline for maker-annotation-eukaryote.ga
+  job:
+    EST and/or cDNA:
+      class: File
+      location: https://zenodo.org/record/5095188/files/cds.fasta?download=1
+    Genome sequence:
+      class: File
+      location: https://zenodo.org/record/5095188/files/genome.fasta?download=1
+    Protein sequences:
+      class: File
+      location: https://zenodo.org/record/5095188/files/proteins.fasta?download=1
+  outputs:
+    BUSCO_full_table_01:
+      class: File
+      file: test-data/BUSCO_full_table_01.tabular
+      compare: diff
+      lines_diff: 4
+    BUSCO_missing_orthologs_01:
+      class: File
+      file: test-data/BUSCO_missing_orthologs_01.tabular
+      compare: diff
+      lines_diff: 4
+    BUSCO_short_summary_01:
+      asserts:
+        has_text: 
+          text: "Complete and single-copy BUSCOs"
+        has_text: 
+          text: "Complete and duplicated BUSCOs"
+    BUSCO_short_summary_02:
+      asserts:
+        has_text: 
+          text: "Complete and single-copy BUSCOs"
+        has_text: 
+          text: "Complete and duplicated BUSCOs"
+    BUSCO_short_summary_03:
+      asserts:
+        has_text: 
+          text: "Complete and single-copy BUSCOs"
+        has_text: 
+          text: "Complete and duplicated BUSCOs"
+    BUSCO_short_summary_04:
+      asserts:
+        has_text: 
+          text: "Complete and single-copy BUSCOs"
+        has_text: 
+          text: "Complete and duplicated BUSCOs"
+    SNAP_trained_model:
+      asserts:
+        has_size: 
+          value: 46205
+          delta: 1000
+    fasta_statistics:
+      asserts:
+        has_size: 
+          value: 206
+          delta: 10
+    genome_annotation_statistics_graphs_01:
+      asserts:
+        has_size: 
+          value: 18850
+          delta: 300
+    genome_annotation_statistics_graphs_02:
+      asserts:
+        has_size: 
+          value: 18857
+          delta: 300
+    genome_annotation_statistics_graphs_03:
+      asserts:
+        has_size: 
+          value: 18944
+          delta: 300
+    genome_annotation_statistics_summary_01:
+      asserts:
+        has_text: 
+          text: "Mean gene locus size (first to last exon)"
+        has_text: 
+          text: "Number of genes with alternative transcript variants"
+    genome_annotation_statistics_summary_02:
+      asserts:
+        has_text: 
+          text: "Mean gene locus size (first to last exon)"
+        has_text: 
+          text: "Number of genes with alternative transcript variants"
+    genome_annotation_statistics_summary_03:
+      asserts:
+        has_text: 
+          text: "Mean gene locus size (first to last exon)"
+        has_text: 
+          text: "Number of genes with alternative transcript variants"
+    gffread_cds:
+      asserts:
+        has_text: 
+          text: ">TEST000001-RA gene=TEST000001"
+        has_text: 
+          text: ">TEST000100-RA gene=TEST000100"
+        has_text: 
+          text: ">TEST000200-RA gene=TEST000200"
+    gffread_exons:
+      asserts:
+        has_text: 
+          text: ">TEST000001-RA gene=TEST000001 CDS"
+        has_text: 
+          text: ">TEST000100-RA gene=TEST000100 CDS"
+        has_text: 
+          text: ">TEST000200-RA gene=TEST000200 CDS"
+    gffread_translated_cds:
+      asserts:
+        has_text: 
+          text: ">TEST000001-RA gene=TEST000001"
+        has_text: 
+          text: ">TEST000100-RA gene=TEST000100"
+        has_text: 
+          text: ">TEST000200-RA gene=TEST000200"
+    map_annotation_ids:
+      asserts:
+        has_text: 
+          text: "NC_003421.2"
+    augus_trained_model:
+      asserts:
+        has_size: 
+          value: 151220
+          delta: 18000