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Added parameter add_attrs_to_proteins_fasta
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@GallVp
GallVp committed Sep 20, 2024
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7 changes: 4 additions & 3 deletions CHANGELOG.md
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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).

## 0.4.0+dev - [13-Sep-2024]
## 0.4.0+dev - [20-Sep-2024]

### `Added`

Expand All @@ -17,7 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
8. Added `GXF_FASTA_AGAT_SPADDINTRONS_SPEXTRACTSEQUENCES` sub-workflow for splice type statistics [#11](https://github.com/plant-food-research-open/genepal/issues/11)
9. Changed `orthofinder_annotations` from FASTA/GFF to protein FASTA [#43](https://github.com/plant-food-research-open/genepal/issues/43)
10. Added param `enforce_full_intron_support` to turn on/off strict model purging by TSEBRA [#21](https://github.com/plant-food-research-open/genepal/issues/21)
11. Added param `filter_liftoff_by_hints` to evaluate liftoff models with TSEBRA to make sure they have the same level of evidence as BRAKER [#28](ttps://github.com/plant-food-research-open/genepal/issues/28)
11. Added param `filter_liftoff_by_hints` to evaluate liftoff models with TSEBRA to make sure they have the same level of evidence as BRAKER [#28](https://github.com/plant-food-research-open/genepal/issues/28)
12. Added a script to automatically check module version updates
13. Reduced `BRAKER3` threads to 8 [#55](https://github.com/plant-food-research-open/genepal/issues/55)
14. Now the final annotations are stored in the `annotations` folder [#53](https://github.com/plant-food-research-open/genepal/issues/53)
Expand All @@ -26,7 +26,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
17. `eggnogmapper_db_dir` is not a required parameter anymore
18. `eggnogmapper_tax_scope` is now set to 1 (root div) by default
19. Added a `test` profile based on public data
20. Updated modules and sub-workflows
20. Added parameter `add_attrs_to_proteins_fasta` to enable/disable addition of decoded gff attributes to proteins fasta [#58](https://github.com/plant-food-research-open/genepal/issues/58)
21. Updated modules and sub-workflows

### `Fixed`

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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -271,7 +271,7 @@ process { // SUBWORKFLOW: GFF_STORE
}

withName: '.*:GFF_STORE:EXTRACT_PROTEINS' {
ext.args = '-y'
ext.args = params.add_attrs_to_proteins_fasta ? '-F -D -y' : '-y'
ext.prefix = { "${meta.id}.pep" }

publishDir = [
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3 changes: 2 additions & 1 deletion local_genepal
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Expand Up @@ -20,4 +20,5 @@ nextflow run \
--max_cpus 8 \
--max_memory '32.GB' \
--eggnogmapper_tax_scope 33090 \
--eggnogmapper_db_dir ../dbs/emapperdb/5.0.2
--eggnogmapper_db_dir ../dbs/emapperdb/5.0.2 \
--outdir results
1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -51,6 +51,7 @@ params {
eggnogmapper_evalue = 0.00001
eggnogmapper_pident = 35
eggnogmapper_purge_nohits = false
add_attrs_to_proteins_fasta = false

// Evaluation options
busco_skip = false
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82 changes: 56 additions & 26 deletions nextflow_schema.json
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Expand Up @@ -38,7 +38,8 @@
"type": "integer",
"description": "Eggnogmapper taxonomy scopre. Eukaryota: 2759, Viridiplantae: 33090, Archaea: 2157, Bacteria: 2, root: 1",
"minimum": 1,
"default": 1
"default": 1,
"fa_icon": "fas fa-hashtag"
},
"rna_evidence": {
"type": "string",
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"type": "string",
"default": "repeatmodeler",
"enum": ["edta", "repeatmodeler"],
"description": "'edta' or 'repeatmodeler'"
"description": "'edta' or 'repeatmodeler'",
"fa_icon": "fas fa-tasks"
},
"save_annotated_te_lib": {
"type": "boolean",
"description": "Save annotated TE library or not?"
"description": "Save annotated TE library or not?",
"fa_icon": "fas fa-question-circle"
},
"edta_is_sensitive": {
"type": "boolean",
"description": "Use '--sensitive 1' flag with EDTA or not?"
"description": "Use '--sensitive 1' flag with EDTA or not?",
"fa_icon": "fas fa-question-circle"
},
"repeatmasker_save_outputs": {
"type": "boolean",
"description": "Save the repeat-masked genome or not?"
"description": "Save the repeat-masked genome or not?",
"fa_icon": "fas fa-question-circle"
}
}
},
"fa_icon": "fab fa-adn"
},
"rnaseq_pre_processing_options": {
"title": "RNASeq pre-processing options",
Expand All @@ -109,33 +115,40 @@
"properties": {
"skip_fastqc": {
"type": "boolean",
"description": "Skip FASTQC or not?"
"description": "Skip FASTQC or not?",
"fa_icon": "fas fa-question-circle"
},
"skip_fastp": {
"type": "boolean",
"description": "Skip trimming by FASTQP or not?"
"description": "Skip trimming by FASTQP or not?",
"fa_icon": "fas fa-question-circle"
},
"min_trimmed_reads": {
"type": "integer",
"default": 10000,
"description": "Exclude a sample if its reads after trimming are below this number",
"minimum": 0
"minimum": 0,
"fa_icon": "fas fa-hashtag"
},
"extra_fastp_args": {
"type": "string",
"description": "Extra FASTP arguments"
"description": "Extra FASTP arguments",
"fa_icon": "fas fa-terminal"
},
"save_trimmed": {
"type": "boolean",
"description": "Save FASTQ files after trimming or not?"
"description": "Save FASTQ files after trimming or not?",
"fa_icon": "fas fa-question-circle"
},
"remove_ribo_rna": {
"type": "boolean",
"description": "Remove Ribosomal RNA or not?"
"description": "Remove Ribosomal RNA or not?",
"fa_icon": "fas fa-question-circle"
},
"save_non_ribo_reads": {
"type": "boolean",
"description": "Save FASTQ files after Ribosomal RNA removal or not?"
"description": "Save FASTQ files after Ribosomal RNA removal or not?",
"fa_icon": "fas fa-question-circle"
},
"ribo_database_manifest": {
"type": "string",
Expand All @@ -146,7 +159,8 @@
"fa_icon": "fas fa-database",
"description": "Ribosomal RNA fastas listed in a text sheet"
}
}
},
"fa_icon": "fas fa-filter"
},
"rnaseq_alignment_options": {
"title": "RNAseq alignment options",
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"type": "integer",
"default": 16000,
"minimum": 0,
"description": "Maximum intron length for STAR alignment"
"description": "Maximum intron length for STAR alignment",
"fa_icon": "fas fa-hashtag"
},
"star_align_extra_args": {
"type": "string",
"description": "EXTRA arguments for STAR"
"description": "EXTRA arguments for STAR",
"fa_icon": "fas fa-terminal"
},
"star_save_outputs": {
"type": "boolean",
"description": "Save BAM files from STAR or not?"
"description": "Save BAM files from STAR or not?",
"fa_icon": "fas fa-question-circle"
},
"save_cat_bam": {
"type": "boolean",
"description": "SAVE a concatenated BAM file per assembly or not?"
"description": "SAVE a concatenated BAM file per assembly or not?",
"fa_icon": "fas fa-question-circle"
}
}
},
"fa_icon": "fas fa-align-center"
},
"annotation_options": {
"title": "Annotation options",
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"properties": {
"braker_extra_args": {
"type": "string",
"description": "Extra arguments for BRAKER"
"description": "Extra arguments for BRAKER",
"fa_icon": "fas fa-terminal"
},
"braker_save_outputs": {
"type": "boolean",
Expand All @@ -194,12 +214,14 @@
"default": 0.9,
"minimum": 0,
"maximum": 1,
"description": "Liftoff coverage parameter"
"description": "Liftoff coverage parameter",
"fa_icon": "fas fa-hashtag"
},
"liftoff_identity": {
"type": "number",
"default": 0.9,
"description": "Liftoff identity parameter"
"description": "Liftoff identity parameter",
"fa_icon": "fas fa-hashtag"
},
"allow_isoforms": {
"type": "boolean",
Expand All @@ -222,20 +244,28 @@
"eggnogmapper_evalue": {
"type": "number",
"default": 1e-5,
"description": "Only report alignments below or equal the e-value threshold"
"description": "Only report alignments below or equal the e-value threshold",
"fa_icon": "fas fa-hashtag"
},
"eggnogmapper_pident": {
"type": "integer",
"default": 35,
"description": "Only report alignments above or equal to the given percentage of identity (0-100)",
"minimum": 0,
"maximum": 100
"maximum": 100,
"fa_icon": "fas fa-hashtag"
},
"eggnogmapper_purge_nohits": {
"type": "boolean",
"description": "Purge transcripts which do not have a hit against eggnog"
"description": "Purge transcripts which do not have a hit against eggnog",
"fa_icon": "fas fa-question-circle"
},
"add_attrs_to_proteins_fasta": {
"type": "boolean",
"fa_icon": "fas fa-question-circle"
}
}
},
"fa_icon": "fab fa-adn"
},
"evaluation_options": {
"title": "Evaluation options",
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