nf-core_modules/deprecated/tcoffee/main.nf

process tcoffee {
    tag "$fasta"
    publishDir "${params.outdir}/tcoffee"
    container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5'

    input:
    path "$fasta"

    output:
    path "${fasta}.aln"

    script:
    """
    t_coffee -seq $fasta -outfile ${fasta}.aln
    """
}
Adding tcoffee module 2020-03-05 16:18:35 +00:00			`process tcoffee {`
Minor style improvents This commit provides a minor refactoring with som Nextflow code style improvments: - Replaces `.toGiga()` with `.giga` - Replaces `tag { foo }` with `tag "$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 "$fasta"`
Changing `publishDir` to take `params.outdir` and modifying `yml` for github actions 2020-03-06 11:23:23 +00:00			`publishDir "${params.outdir}/tcoffee"`
Adding tcoffee module 2020-03-05 16:18:35 +00:00			`container 'quay.io/biocontainers/t_coffee:11.0.8--py27pl5.22.0_5'`

			`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 "$foo"` - Move publishDir before input declarations. Directives should be before the first input. Tho this is not enforced, it may be in future versions. - Replaces input `file` with `path` - Remove unnecessary parentheses 2020-07-27 10:11:42 +00:00			`path "$fasta"`
Adding tcoffee module 2020-03-05 16:18:35 +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 "$foo"` - Move publishDir before input declarations. Directives should be before the first input. Tho this is not enforced, it may be in future versions. - Replaces input `file` with `path` - Remove unnecessary parentheses 2020-07-27 10:11:42 +00:00			`path "${fasta}.aln"`
Adding tcoffee module 2020-03-05 16:18:35 +00:00
			`script:`
			`"""`
			`t_coffee -seq $fasta -outfile ${fasta}.aln`
			`"""`
			`}`