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🧸 Updated rasusa (#437)

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* changed genome size input position

* fixed...😊
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Thanh Lee 2021-04-12 21:47:55 +01:00 committed by GitHub
parent c99ab09f8d
commit c736817598
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3 changed files with 7 additions and 8 deletions
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3
software/rasusa/main.nf
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@ -19,9 +19,8 @@ process RASUSA {
} }
input: input:
tuple val(meta), path(reads) tuple val(meta), path(reads), val(genome_size)
val depth_cutoff val depth_cutoff
val genome_size
output: output:
tuple val(meta), path('*.fastq.gz'), emit: reads tuple val(meta), path('*.fastq.gz'), emit: reads

6
software/rasusa/meta.yml
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@ -22,12 +22,12 @@ input:
- reads: - reads:
type: file type: file
description: List of input paired-end FastQ files description: List of input paired-end FastQ files
- depth_cutoff:
type: integer
description: Depth of coverage cutoff
- genome_size: - genome_size:
type: string type: string
description: Genome size of the species description: Genome size of the species
- depth_cutoff:
type: integer
description: Depth of coverage cutoff
output: output:
- meta: - meta:

6
tests/software/rasusa/main.nf
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@ -8,11 +8,11 @@ workflow test_rasusa {
input = [ [ id:'test', single_end:false], // meta map input = [ [ id:'test', single_end:false], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
] ],
"1000000b"
] ]
depth_cutoff = 100 depth_cutoff = 100
genome_size = "1000000b"
RASUSA ( input, depth_cutoff, genome_size ) RASUSA ( input, depth_cutoff )
} }