Add Maker annotation workflow #47
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| version: 1.2 | ||
| workflows: | ||
| - name: "ANNOTATION-OF-EUKARYOTIC-GENOMES-WITH-MAKER" | ||
|
There was a problem hiding this comment. Any particular reason to have this name in upper case? There was a problem hiding this comment. 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 |
||
| 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 |
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| 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 |
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| Annotation of eukaryotic genomes with MAKER | ||
| ------------------------------------------- | ||
|
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| 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). |
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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/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 | ||
| location: https://zenodo.org/record/5095188/files/BUSCO_full_table_01.tabular?download=1 | ||
| compare: diff | ||
| lines_diff: 4 | ||
| BUSCO_missing_orthologs_01: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/BUSCO_missing_orthologs_01.tabular?download=1 | ||
| compare: diff | ||
| lines_diff: 4 | ||
| BUSCO_short_summary_01: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/BUSCO_short_summary_01.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| BUSCO_short_summary_02: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/BUSCO_short_summary_02.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| BUSCO_short_summary_03: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/BUSCO_short_summary_03.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| BUSCO_short_summary_04: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/BUSCO_short_summary_04.txt?download=1 | ||
| compare: diff | ||
| lines_diff: 6 | ||
| SNAP_trained_model: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/SNAP_trained_model.snaphmm?download=1 | ||
| compare: size | ||
| delta: 10 | ||
| fasta_statistics: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/fasta_statistics.tabular?download=1 | ||
| compare: size | ||
| genome_annotation_statistics_graphs_01: | ||
| asserts: | ||
| has_size: | ||
| size: 18719 | ||
| delta: 100 | ||
| genome_annotation_statistics_graphs_02: | ||
| asserts: | ||
| has_size: | ||
| size: 18767 | ||
| delta: 100 | ||
| genome_annotation_statistics_graphs_03: | ||
| asserts: | ||
| has_size: | ||
| size: 18958 | ||
| delta: 100 | ||
| genome_annotation_statistics_summary_01: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/genome_annotation_statistics_summary_01.txt?download=1 | ||
| genome_annotation_statistics_summary_02: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/genome_annotation_statistics_summary_02.txt?download=1 | ||
| genome_annotation_statistics_summary_03: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/genome_annotation_statistics_summary_03.txt?download=1 | ||
| gffread_cds: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/gffread_cds.fasta?download=1 | ||
| compare: size | ||
| gffread_exons: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/gffread_exons.fasta?download=1 | ||
| compare: size | ||
| gffread_translated_cds: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/gffread_translated_cds.fasta?download=1 | ||
| compare: size | ||
| map_annotation_ids: | ||
| class: File | ||
| location: https://zenodo.org/record/5095188/files/map_annotation_ids.gff3?download=1 | ||
| compare: size | ||
| jbrowse_report: | ||
| asserts: | ||
| has_size: | ||
| size: 2483977 | ||
| delta: 100 | ||
| augus_trained_model: | ||
| asserts: | ||
| has_size: | ||
| size: 46222 | ||
| delta: 100 |
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masteris a moving target. Ideally this should be changed to pin a specific release before the PR is merged.