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Merge pull request #122 from Plant-Food-Research-Open/patch/121
Fixed TSEBRA failure issue
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| Original file line number | Diff line number | Diff line change |
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@@ -3,11 +3,26 @@ | |
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) | ||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## v0.6.0 - [4-Dec-2024] | ||
| ## v0.6.0 - [6-Dec-2024] | ||
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| ### 'Added' | ||
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| 1. Added cDNA and CDS outputs to <OUTPUT_DIR>/annotations/<SAMPLE> directory [#118](https://github.com/Plant-Food-Research-Open/genepal/issues/118) | ||
| 2. Added parameter `add_attrs_to_proteins_cds_fastas` | ||
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| ### `Fixed` | ||
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| 1. Fixed an issue where TSEBRA failed because LIFTOFF lifted non-protein coding genes [#121](https://github.com/Plant-Food-Research-Open/genepal/issues/121) | ||
| 2. Switched branch name from `master` to `main` in the GHA CIs | ||
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| ### `Dependencies` | ||
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| 1. Nextflow!>=24.04.2 | ||
| 2. [email protected] | ||
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| ### `Deprecated` | ||
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| 1. Removed parameter `add_attrs_to_proteins_fasta` | ||
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| ## v0.5.0 - [21-Nov-2024] | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,105 @@ | ||
| nextflow_workflow { | ||
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| name "Test Subworkflow FASTA_LIFTOFF" | ||
| script "../main.nf" | ||
| workflow "FASTA_LIFTOFF" | ||
| config './nextflow.config' | ||
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| tag "subworkflows" | ||
| tag "subworkflows_gallvp" | ||
| tag "subworkflows/fasta_liftoff" | ||
| tag "subworkflows/gff_tsebra_spfilterfeaturefromkilllist" | ||
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| tag "gunzip" | ||
| tag "gffread" | ||
| tag "liftoff" | ||
| tag "agat" | ||
| tag "agat/spmergeannotations" | ||
| tag "agat/spflagshortintrons" | ||
| tag "agat/spfilterfeaturefromkilllist" | ||
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| setup { | ||
| run('GUNZIP', alias: 'GUNZIP_GENOME_FASTA') { | ||
| script "../../../../modules/nf-core/gunzip" | ||
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| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.fasta.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
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| run('GUNZIP', alias: 'GUNZIP_BRAKER_HINTS') { | ||
| script "../../../../modules/nf-core/gunzip" | ||
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| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.modules_testdata_base_path + 'genomics/eukaryotes/actinidia_chinensis/genome/chr1/genome.hints.gff.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
| } | ||
| } | ||
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| test("liftoff - GCF_019202715 - to - actinidia_chinensis") { | ||
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| when { | ||
| workflow { | ||
| """ | ||
| input[0] = GUNZIP_GENOME_FASTA.out.gunzip | ||
| input[1] = Channel.of([ | ||
| [ id:'ref' ], | ||
| file ( "${baseDir}/subworkflows/local/fasta_liftoff/tests/testdata/GCF_019202715.1.fna.gz", checkIfExists: true ) | ||
| ]) | ||
| input[2] = Channel.of([ | ||
| [ id:'ref' ], | ||
| file ( "${baseDir}/subworkflows/local/fasta_liftoff/tests/testdata/GCF_019202715.1.gff.gz", checkIfExists: true ) | ||
| ]) | ||
| input[3] = true // val_filter_liftoff_by_hints | ||
| input[4] = GUNZIP_BRAKER_HINTS.out.gunzip | ||
| input[5] = Channel.of ( file("${baseDir}/assets/tsebra-template.cfg", checkIfExists: true) ) | ||
| | map { cfg -> | ||
| def enforce_full_intron_support = true | ||
| def param_intron_support = enforce_full_intron_support ? '1.0' : '0.0' | ||
| def param_e1 = params.allow_isoforms ? '0.1' : '0.0' | ||
| def param_e2 = params.allow_isoforms ? '0.5' : '0.0' | ||
| def param_e3 = params.allow_isoforms ? '0.05' : '0.0' | ||
| def param_e4 = params.allow_isoforms ? '0.2' : '0.0' | ||
| [ | ||
| 'tsebra-config.cfg', | ||
| cfg | ||
| .text | ||
| .replace('PARAM_INTRON_SUPPORT', param_intron_support) | ||
| .replace('PARAM_E1', param_e1) | ||
| .replace('PARAM_E2', param_e2) | ||
| .replace('PARAM_E3', param_e3) | ||
| .replace('PARAM_E4', param_e4) | ||
| ] | ||
| } | ||
| | collectFile | ||
| input[6] = false // val_allow_isoforms | ||
| """ | ||
| } | ||
| } | ||
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| then { | ||
| assertAll( | ||
| { assert workflow.success}, | ||
| { assert snapshot(workflow.out).match()} | ||
| ) | ||
| } | ||
| } | ||
| } |
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