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restoring testdata base path to what it was
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@tanyasarkjain
tanyasarkjain committed Nov 26, 2024
1 parent b0ce95b commit 240dda8
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Showing 5 changed files with 22 additions and 22 deletions.
12 changes: 6 additions & 6 deletions conf/test.config
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Original file line number Diff line number Diff line change
Expand Up @@ -22,16 +22,16 @@ params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function'

input = params.pipelines_testdata_base_path + 'pacbio_data/samplesheet_longread_puretarget.csv'
input = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/samplesheet_longread_puretarget.csv'

//added fasta
fasta = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.fa'
fasta_fai = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.fa.fai'
fasta = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.fa'
fasta_fai = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.fa.fai'

// Additional flags - interval can be null
barcodes = params.pipelines_testdata_base_path + 'pacbio_data/barcodes_D01.fasta'
intervals = params.pipelines_testdata_base_path + 'pacbio_data/c9orf72-short.bed'
barcodes = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/barcodes_D01.fasta'
intervals = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/c9orf72-short.bed'
workflow = 'repeat'
repeat_id = 'C9ORF72'
repeat_id = 'C9ORF72'

}
6 changes: 3 additions & 3 deletions conf/test_full.config
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Expand Up @@ -22,12 +22,12 @@ params {
config_profile_name = 'Full test profile'
config_profile_description = 'Full test dataset to check pipeline function'

input = params.pipelines_testdata_base_path + 'pacbio_data/samplesheet_longread_puretarget.csv'
input = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/samplesheet_longread_puretarget.csv'
genome = 'GATK.GRCh38'

// Additional flags - interval can be null
barcodes = params.pipelines_testdata_base_path + 'pacbio_data/barcodes_D01.fasta'
barcodes = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/barcodes_D01.fasta'
snv_caller = 'gatk4'
workflow = 'wgs'
intervals = params.pipelines_testdata_base_path + 'pacbio_data/intervals.bed'
intervals = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/intervals.bed'
}
12 changes: 6 additions & 6 deletions conf/test_wgs_deepvariant.config
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Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,16 @@ params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function for pure-trgt workflow'

input = params.pipelines_testdata_base_path + 'pacbio_data/subset_samplesheet_longread_puretarget.csv'
fasta = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.fa'
fasta_fai = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.fa.fai'
input = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/subset_samplesheet_longread_puretarget.csv'
fasta = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.fa'
fasta_fai = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.fa.fai'
genome = 'GATK.GRCh38'
dict = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.dict'
dict = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.dict'
dbsnp = ''
dbsnp_tbi = ''
barcodes = params.pipelines_testdata_base_path + 'pacbio_data/barcodes_D01.fasta'
barcodes = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/barcodes_D01.fasta'
snv_caller = 'deepvariant'
intervals = params.pipelines_testdata_base_path + 'pacbio_data/c9orf72-short.bed'
intervals = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/c9orf72-short.bed'
workflow = 'wgs'
skip_phase = true
}
12 changes: 6 additions & 6 deletions conf/test_wgs_gatk.config
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Original file line number Diff line number Diff line change
Expand Up @@ -23,16 +23,16 @@ params {
config_profile_name = 'Test profile'
config_profile_description = 'Minimal test dataset to check pipeline function for pure-trgt workflow'

input = params.pipelines_testdata_base_path + 'pacbio_data/subset_samplesheet_longread_puretarget.csv'
fasta = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.fa'
fasta_fai = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.fa.fai'
input = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/subset_samplesheet_longread_puretarget.csv'
fasta = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.fa'
fasta_fai = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.fa.fai'
genome = 'GATK.GRCh38'
dict = params.pipelines_testdata_base_path + 'pacbio_data/C9ORF72-12.dict'
dict = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/C9ORF72-12.dict'
dbsnp = ''
dbsnp_tbi = ''
barcodes = params.pipelines_testdata_base_path + 'pacbio_data/barcodes_D01.fasta'
barcodes = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/barcodes_D01.fasta'
snv_caller = 'gatk4'
intervals = params.pipelines_testdata_base_path + 'pacbio_data/c9orf72-short.bed'
intervals = params.pipelines_testdata_base_path + 'refs/heads/pacvar/pacbio_data/c9orf72-short.bed'
workflow = 'wgs'
skip_phase = true
}
2 changes: 1 addition & 1 deletion nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,7 @@ params {
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/pacvar/'
pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'

// Config options
config_profile_name = null
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