nf-core_modules/tests/software/spades/main.nf
Harshil Patel acb1a12a56
Re-organise all test data (#354)
* Re-organise all test data

* Fix ECLint

* Fix ECLint agaaainn

* Now is not the time EClint
2021-03-24 09:53:41 +00:00

44 lines
1.5 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] )
workflow test_spades_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ]
]
coronaspades = false
SPADES ( input, [], coronaspades )
}
workflow test_spades_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ]
]
coronaspades = false
SPADES ( input, [], coronaspades )
}
workflow test_coronospades_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true) ]
]
coronaspades = true
SPADES ( input, [], coronaspades )
}
workflow test_coronospades_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true) ]
]
coronaspades = true
SPADES ( input, [], coronaspades )
}