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antismashlite: Support GBK input (#1840)
* 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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2 changed files with 7 additions and 3 deletions
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@ -45,11 +45,12 @@ process ANTISMASH_ANTISMASHLITE {
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script:
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script:
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def args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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prefix = task.ext.suffix ? "${meta.id}${task.ext.suffix}" : "${meta.id}"
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gff_flag = "--genefinding-gff3 ${gff}"
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gff_flag = gff ? "--genefinding-gff3 ${gff}" : ""
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"""
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"""
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## We specifically do not include annotations (--genefinding-tool none) as
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## We specifically do not include on-the-fly annotations (--genefinding-tool none) as
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## this should be run as a separate module for versioning purposes
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## this should be run as a separate module for versioning purposes
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antismash \\
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antismash \\
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$args \\
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$args \\
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$gff_flag \\
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$gff_flag \\
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@ -37,7 +37,9 @@ input:
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pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
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pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}"
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- databases:
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- databases:
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type: directory
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type: directory
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description: downloaded AntiSMASH databases e.g. data/databases
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description: |
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Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory
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"data/databases")
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pattern: "*/"
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pattern: "*/"
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- antismash_dir:
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- antismash_dir:
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type: directory
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type: directory
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@ -51,6 +53,7 @@ input:
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pattern: "*/"
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pattern: "*/"
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- gff:
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- gff:
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type: file
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type: file
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description: Annotations in GFF3 format (only if sequence_input is in FASTA format)
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pattern: "*.gff"
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pattern: "*.gff"
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output:
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output:
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