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antismashlite: Support GBK input (#1840)

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* Support non-GFF input

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Fix linting error

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Jasmin F 2022-07-01 09:29:53 +02:00 committed by GitHub
parent b96066565a
commit b3acfc54f5
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2 changed files with 7 additions and 3 deletions
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5
modules/antismash/antismashlite/main.nf
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@ -45,11 +45,12 @@ process ANTISMASH_ANTISMASHLITE {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}" prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
gff_flag = "--genefinding-gff3 ${gff}" gff_flag = gff ? "--genefinding-gff3 ${gff}" : ""
""" """
## We specifically do not include annotations (--genefinding-tool none) as ## We specifically do not include on-the-fly annotations (--genefinding-tool none) as
## this should be run as a separate module for versioning purposes ## this should be run as a separate module for versioning purposes
antismash \\ antismash \\
$args \\ $args \\
$gff_flag \\ $gff_flag \\

5
modules/antismash/antismashlite/meta.yml
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@ -37,7 +37,9 @@ input:
pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
- databases: - databases:
type: directory type: directory
description: downloaded AntiSMASH databases e.g. data/databases description: |
Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory
"data/databases")
pattern: "*/" pattern: "*/"
- antismash_dir: - antismash_dir:
type: directory type: directory
@ -51,6 +53,7 @@ input:
pattern: "*/" pattern: "*/"
- gff: - gff:
type: file type: file
description: Annotations in GFF3 format (only if sequence_input is in FASTA format)
pattern: "*.gff" pattern: "*.gff"
output: output: