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changed 'covid' to 'sarscov2'

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kevinmenden 2021-01-29 12:45:21 +01:00
parent 3390f7621d
commit 9156becd19
6 changed files with 11 additions and 11 deletions
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tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna → tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna
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tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_genomic.fna → tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna
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tests/data/fastq/rna/covid/EPI_ISL_486436_1.fastq.gz → tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz
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tests/data/fastq/rna/covid/EPI_ISL_486436_2.fastq.gz → tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz
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tests/data/gff/covid/GCA_011545545.1_ASM1154554v1_genomic.gtf → tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf
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22
tests/software/salmon/main.nf
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@ -6,29 +6,29 @@ include { SALMON_INDEX } from '../../../software/salmon/index/main.nf' addParams
include { SALMON_QUANT } from '../../../software/salmon/quant/main.nf' addParams( options: quant_options )
workflow test_salmon_index {
genome_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
SALMON_INDEX ( genome_fasta, transcript_fasta )
}
workflow test_salmon_quant_pe {
genome_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/covid/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
input = [ [ id:'test', single_end:false ], // meta map
[ file("${launchDir}/tests/data/fastq/rna/covid/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/covid/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
[ file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true),
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_2.fastq.gz", checkIfExists: true) ] ]
SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)
}
workflow test_salmon_quant_se {
genome_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/covid/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/covid/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
genome_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.fna", checkIfExists: true)
transcript_fasta = file("${launchDir}/tests/data/fasta/sarscov2/GCA_011545545.1_ASM1154554v1_cds_from_genomic.fna", checkIfExists: true)
gtf = file("${launchDir}/tests/data/gff/sarscov2/GCA_011545545.1_ASM1154554v1_genomic.gtf", checkIfExists: true)
input = [ [ id:'test', single_end:true ], // meta map
file("${launchDir}/tests/data/fastq/rna/covid/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
file("${launchDir}/tests/data/fastq/rna/sarscov2/EPI_ISL_486436_1.fastq.gz", checkIfExists: true) ]
SALMON_INDEX ( genome_fasta, transcript_fasta )
SALMON_QUANT( input, SALMON_INDEX.out.index, gtf, transcript_fasta, false)