nf-core_modules/software/shovill/main.nf

process shovill {

    tag "$shovill"

    publishDir "${params.outdir}", pattern: '*.fasta', mode: 'copy'

    container "quay.io/biocontainers/shovill:1.0.9--0"

    input:
    tuple val(sample_id), path(forward), path(reverse)

    output:
    path "${sample_id}.fasta"

    script:
    """
    shovill --R1 ${forward} --R2 ${reverse} --outdir shovill_out
    mv shovill_out/contigs.fa ${sample_id}.fasta
    """
}
initial commit of shovill 2020-03-05 09:29:23 +00:00			`process shovill {`

Minor style improvents This commit provides a minor refactoring with som Nextflow code style improvments: - Replaces `.toGiga()` with `.giga` - Replaces `tag { foo }` with `tag "$foo"` - Move publishDir before input declarations. Directives should be before the first input. Tho this is not enforced, it may be in future versions. - Replaces input `file` with `path` - Remove unnecessary parentheses 2020-07-27 10:11:42 +00:00			`tag "$shovill"`
initial commit of shovill 2020-03-05 09:29:23 +00:00
			`publishDir "${params.outdir}", pattern: '*.fasta', mode: 'copy'`
Fix editor config styles 2020-07-11 11:42:13 +00:00
initial commit of shovill 2020-03-05 09:29:23 +00:00			`container "quay.io/biocontainers/shovill:1.0.9--0"`

			`input:`
Minor style improvents This commit provides a minor refactoring with som Nextflow code style improvments: - Replaces `.toGiga()` with `.giga` - Replaces `tag { foo }` with `tag "$foo"` - Move publishDir before input declarations. Directives should be before the first input. Tho this is not enforced, it may be in future versions. - Replaces input `file` with `path` - Remove unnecessary parentheses 2020-07-27 10:11:42 +00:00			`tuple val(sample_id), path(forward), path(reverse)`
initial commit of shovill 2020-03-05 09:29:23 +00:00
			`output:`
Minor style improvents This commit provides a minor refactoring with som Nextflow code style improvments: - Replaces `.toGiga()` with `.giga` - Replaces `tag { foo }` with `tag "$foo"` - Move publishDir before input declarations. Directives should be before the first input. Tho this is not enforced, it may be in future versions. - Replaces input `file` with `path` - Remove unnecessary parentheses 2020-07-27 10:11:42 +00:00			`path "${sample_id}.fasta"`
Fix editor config styles 2020-07-11 11:42:13 +00:00
initial commit of shovill 2020-03-05 09:29:23 +00:00			`script:`
			`"""`
			`shovill --R1 ${forward} --R2 ${reverse} --outdir shovill_out`
			`mv shovill_out/contigs.fa ${sample_id}.fasta`
			`"""`
			`}`