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Patch issue100 #101

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merged 4 commits into from
Nov 17, 2023
Merged

Patch issue100 #101

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0fba4c3
Update default merge_annotation_identifier
mahesh-panchal Nov 8, 2023
30a8b14
Add pcds parameter
mahesh-panchal Nov 8, 2023
78e68ad
Update merge functional annotation args
mahesh-panchal Nov 8, 2023
94b3967
Update README with parameter descriptions
mahesh-panchal Nov 8, 2023
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5 changes: 3 additions & 2 deletions config/functional_annotation_modules.config
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Expand Up @@ -27,8 +27,9 @@ process {
}
withName: 'MERGE_FUNCTIONAL_ANNOTATION' {
ext.args = [
'-id NBIS',
'-pe 5'
"-id $params.merge_annotation_identifier",
'-pe 5',
params.use_pcds ? "--pcds" : ""
].join(' ').trim()
publishDir = [
[
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3 changes: 2 additions & 1 deletion nextflow.config
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Expand Up @@ -33,7 +33,8 @@ params {
gff_annotation = '/path/to/annotation.gff'
records_per_file = 1000
blast_db_fasta = '/path/to/protein/database.fasta'
merge_annotation_identifier = 'ID'
merge_annotation_identifier = 'NBIS'
use_pcds = false

// Transcript assembly parameters
reads = "/path/to/reads_{1,2}.fastq.gz"
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3 changes: 3 additions & 0 deletions subworkflows/functional_annotation/README.md
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Expand Up @@ -51,6 +51,9 @@ nextflow run NBISweden/pipelines-nextflow \
- `outdir`: Path to the results folder.
- `records_per_file`: Number of fasta records per file to distribute to blast and interproscan (default: 1000).
- `codon_table`: (default: 1).
- `blast_db_fasta` : Path to blast protein database fasta.
- `merge_annotation_identifier`: The identifier to use for labeling genes (default: NBIS).
- `use_pcds`: If true, enables the pcds flag when merging annotation.

### Tool specific parameters

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