nf-core_modules/tests/software/plasmidid/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { PLASMIDID } from '../../../software/plasmidid/main.nf' addParams ( options: ['args' : '-k 0.8'] )

workflow test_plasmidid {

    contigs = [ [ id:'test' ], // meta map
                file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)
              ]

    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

    PLASMIDID ( contigs, fasta )
}
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml 2021-04-08 21:44:30 +00:00			`#!/usr/bin/env nextflow`

			`nextflow.enable.dsl = 2`

			`include { PLASMIDID } from '../../../software/plasmidid/main.nf' addParams ( options: ['args' : '-k 0.8'] )`

			`workflow test_plasmidid {`

			`contigs = [ [ id:'test' ], // meta map`
Move assembly test files from genome to illumina (#441) * FIx plasmidid tests for new contigs.fasta file * Fixing two md5sum hashes * Update test path in config for illumina assembly files * Update modules using assembly files * Correctly setting path of assembly files * Update tests/config/test_data.config Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com> 2021-04-13 10:52:11 +00:00			`file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true)`
Add plasmidid module (#410) * Adding plasmidid module * Adding test for plasmidid module * Update plasmidid version to 1.6.4 * Adding contigs.fasta file * Update tests * Adding output files on test.yml 2021-04-08 21:44:30 +00:00			`]`

			`fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)`

			`PLASMIDID ( contigs, fasta )`
			`}`