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updated reference paths and UMI param names in test_full.config #165

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updated reference paths and UMI param names in test_full.config #165

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c5d3028
updated reference paths and UMI param names in test_full.config
iraiosub Apr 4, 2025
5ccf038
fixed indentation
iraiosub Apr 4, 2025
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15 changes: 9 additions & 6 deletions conf/test_full.config
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Original file line number Diff line number Diff line change
Expand Up @@ -17,13 +17,16 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/clipseq/refs/heads/feat-2-0/tests/test_new_samplesheet_FASTQ_full.csv'
input = 'https://raw.githubusercontent.com/nf-core/clipseq/refs/heads/feat-2-0/tests/test_new_samplesheet_FASTQ_full.csv'
source = "fastq"

// Genome references
ncrna_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/v_2_0/genome/homosapiens_smallRNA.fa.gz"
fasta = 's3://ngi-igenomes/test-data/clipseq/input_data/reference/GRCh38.primary_assembly.genome.fa.gz'
gtf = 's3://ngi-igenomes/test-data/clipseq/input_data/reference/gencode.v37.primary_assembly.annotation.gtf.gz'
move_umi = 'NNNNNNNNN'
umi_separator = '_'
ncrna_fasta = "https://raw.githubusercontent.com/nf-core/test-datasets/clipseq/v_2_0/genome/homosapiens_smallRNA.fa.gz"
fasta = 'https://ftp.ensembl.org/pub/release-111/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz'
gtf = 'https://ftp.ensembl.org/pub/release-111/gtf/homo_sapiens/Homo_sapiens.GRCh38.111.gtf.gz'

// UMI options
umitools_bc_pattern = 'NNNNNNNNN'
umitools_umi_separator = '_'
skip_umi_extract = false
}
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