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Add Maker annotation workflow #47
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15bea80
Add maker annotation workflow
gallardoalba 6f792e3
Update workflow name in yml file
gallardoalba 41a2064
Update title and dockstore file
gallardoalba 1118a0c
Modify dockstore file
gallardoalba bcef099
Fix tests
gallardoalba b81d7e6
Fix tests
gallardoalba 4cb151b
Update datasets
gallardoalba 97acc4a
Use planemo from master branch for tests
mvdbeek b0d0d47
Include tar in augustus conda package
gallardoalba 6ca5807
Update workflow Augustus 3.4
gallardoalba 4d5d81a
Update tests include files
gallardoalba af8899c
Remove unnecesary file
gallardoalba 2cac706
Fix tests replace size by value
gallardoalba 9d43494
Update tests
gallardoalba 3daee38
Revert "Use planemo from master branch for tests"
mvdbeek d535a55
Move maker-annotation-eukaryote into genome-annotation
mvdbeek dc2e56a
Also drop remaining exact comparisons
mvdbeek 1356592
More test fixes
mvdbeek 1ee8509
Update last tests
gallardoalba dce532d
Update README.md
gallardoalba 1e08ee3
Update CHANGELOG.md
gallardoalba 75c735b
Update workflows/genome-annotation/maker-annotation-eukaryote/README.md
gallardoalba e72d7ff
Update README.md: include licencing
gallardoalba eda05ed
Update CHANGELOG.md
gallardoalba 6d106b2
Update workflows/genome-annotation/maker-annotation-eukaryote/README.md
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| version: 1.2 | ||
| workflows: | ||
| - name: "ANNOTATION-OF-EUKARYOTIC-GENOMES-WITH-MAKER" | ||
| primaryDescriptorPath: /maker-annotation-eukaryote.ga | ||
| subclass: Galaxy | ||
| testParameterFiles: | ||
| - /maker-annotation-eukaryote-tests.yml | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| 0.1 | ||
| --------- | ||
| - Initial version of Annotation of eukaryotic genomes with MAKER workflow |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| Annotation of eukaryotic genomes with MAKER | ||
| ------------------------------------------- | ||
|
|
||
| This workflow describes the necessary steps to annotate eukaryotic genomes. 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). |
101 changes: 101 additions & 0 deletions
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workflows/maker-annotation/maker-annotation-eukaryote-tests.yml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,101 @@ | ||
| - doc: Test outline for maker-annotation-eukaryote.ga | ||
| job: | ||
| EST and/or cDNA: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/cds.fasta?download=1 | ||
| Genome sequence: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/genome.fasta?download=1 | ||
| Protein sequences: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/proteins.fasta?download=1 | ||
| outputs: | ||
| BUSCO_full_table_01: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/BUSCO_full_table_01.tabular?download=1 | ||
| compare: diff | ||
| lines_diff: 4 | ||
| BUSCO_missing_orthologs_01: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/BUSCO_missing_orthologs_01.tabular?download=1 | ||
| compare: diff | ||
| lines_diff: 4 | ||
| BUSCO_short_summary_01: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/BUSCO_short_summary_01.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| BUSCO_short_summary_02: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/BUSCO_short_summary_02.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| BUSCO_short_summary_03: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/BUSCO_short_summary_03.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| BUSCO_short_summary_04: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/BUSCO_short_summary_04.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| SNAP_trained_model: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/SNAP_trained_model.snaphmm?download=1 | ||
| compare: size | ||
| delta: 10 | ||
| fasta_statistics: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/fasta_statistics.tabular?download=1 | ||
| compare: size | ||
| genome_annotation_statistics_graphs_01: | ||
| asserts: | ||
| has_size: | ||
| size: 18804 | ||
| delta: 100 | ||
| genome_annotation_statistics_graphs_02: | ||
| asserts: | ||
| has_size: | ||
| size: 18901 | ||
| delta: 100 | ||
| genome_annotation_statistics_graphs_03: | ||
| asserts: | ||
| has_size: | ||
| size: 18796 | ||
| delta: 100 | ||
| genome_annotation_statistics_summary_01: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/genome_annotation_statistics_summary_01.txt?download=1 | ||
| genome_annotation_statistics_summary_02: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/genome_annotation_statistics_summary_02.txt?download=1 | ||
| genome_annotation_statistics_summary_03: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/genome_annotation_statistics_summary_03.txt?download=1 | ||
| gffread_cds: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/gffread_cds.fasta?download=1 | ||
| compare: size | ||
| gffread_exons: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/gffread_exons.fasta?download=1 | ||
| compare: size | ||
| gffread_translated_cds: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/gffread_translated_cds.fasta?download=1 | ||
| compare: size | ||
| map_annotation_ids: | ||
| class: File | ||
| location: https://zenodo.org/record/5090816/files/map_annotation_ids.gff3?download=1 | ||
| compare: size | ||
| jbrowse_report: | ||
| asserts: | ||
| has_size: | ||
| size: 4667609 | ||
| delta: 100 | ||
| augus_trained_model: | ||
| asserts: | ||
| has_size: | ||
| size: 183615 | ||
| delta: 100 |
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Any particular reason to have this name in upper case?
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Not really, except that we named all the covid-19 workflows in uppercase, but there's no technical reason to do it. If there's only a single workflow in the folder we could also just call it
main? The only concern is that the name should be reasonably short (if you need to type it manually, or include it as a reference in a paper), and if we add multiple workflows we should know which workflow does what.