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update testdata base path
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@ggabernet
ggabernet committed May 28, 2024
1 parent f2c1a4a commit 50df308
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Showing 15 changed files with 53 additions and 53 deletions.
10 changes: 5 additions & 5 deletions conf/test.config
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Expand Up @@ -20,11 +20,11 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta'
vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

mode = 'fastq'

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4 changes: 2 additions & 2 deletions conf/test_10x_sc.config
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Expand Up @@ -23,6 +23,6 @@ params {


// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-sc/10x_sc_raw.tsv'
reference_10x = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz'
input = pipelines_testdata_base_path + 'airrflow/testdata-sc/10x_sc_raw.tsv'
reference_10x = pipelines_testdata_base_path + 'airrflow/testdata-sc/refdata-cellranger-vdj-GRCh38-alts-ensembl-5.0.0.tar.gz'
}
6 changes: 3 additions & 3 deletions conf/test_assembled_hs.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_assembled_immcantation_devel_hs.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_hs.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_assembled_immcantation_devel_mm.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_assembled_mm.config
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Expand Up @@ -18,9 +18,9 @@ params {

// Input data
mode = 'assembled'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-reveal/test_assembled_metadata_mm.tsv'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

reassign = true
productive_only = true
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6 changes: 3 additions & 3 deletions conf/test_clontech_umi.config
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Expand Up @@ -21,10 +21,10 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-clontech/samplesheet.tsv'
input = pipelines_testdata_base_path +'airrflow/testdata-clontech/samplesheet.tsv'

reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

clonal_threshold = 0.1

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6 changes: 3 additions & 3 deletions conf/test_fetchimgt.config
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Expand Up @@ -20,9 +20,9 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta'
vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta'
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'
fetch_imgt = true

mode = 'fastq'
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6 changes: 3 additions & 3 deletions conf/test_full.config
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Expand Up @@ -15,11 +15,11 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/metadata_pcr_umi_airr_300.tsv'
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/metadata_pcr_umi_airr_300.tsv'
cprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/cprimers.fasta'
vprimers = 's3://ngi-igenomes/test-data/airrflow/pcr_umi/vprimers.fasta'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

lineage_trees = true

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6 changes: 3 additions & 3 deletions conf/test_nebnext_umi.config
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Expand Up @@ -22,10 +22,10 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-neb/samplesheet.tsv'
input = pipelines_testdata_base_path + 'airrflow/testdata-neb/samplesheet.tsv'

reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

clonal_threshold = 0.1

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10 changes: 5 additions & 5 deletions conf/test_no_umi.config
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Expand Up @@ -27,11 +27,11 @@ params {
isotype_column = 'c_primer'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-no-umi/Metadata_test-no-umi_airr.tsv'
cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-no-umi/Greiff2014_CPrimers.fasta'
vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-no-umi/Greiff2014_VPrimers.fasta'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Metadata_test-no-umi_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_CPrimers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-no-umi/Greiff2014_VPrimers.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'


}
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10 changes: 5 additions & 5 deletions conf/test_nocluster.config
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Expand Up @@ -20,11 +20,11 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta'
vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

mode = 'fastq'

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10 changes: 5 additions & 5 deletions conf/test_raw_immcantation_devel.config
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Expand Up @@ -20,12 +20,12 @@ params {
max_time = '6.h'

// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/C_primers.fasta'
vprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-bcr/V_primers.fasta'
input = pipelines_testdata_base_path + 'airrflow/testdata-bcr/Metadata_test_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/C_primers.fasta'
vprimers = pipelines_testdata_base_path + 'airrflow/testdata-bcr/V_primers.fasta'

reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

mode = 'fastq'

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10 changes: 5 additions & 5 deletions conf/test_tcr.config
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Expand Up @@ -28,11 +28,11 @@ params {


// Input data
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-tcr/TCR_metadata_airr.tsv'
cprimers = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-tcr/cprimers.fasta'
race_linker = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/testdata-tcr/linker.fasta'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
input = pipelines_testdata_base_path + 'airrflow/testdata-tcr/TCR_metadata_airr.tsv'
cprimers = pipelines_testdata_base_path + 'airrflow/testdata-tcr/cprimers.fasta'
race_linker = pipelines_testdata_base_path + 'airrflow/testdata-tcr/linker.fasta'
reference_fasta = pipelines_testdata_base_path + 'airrflow/database-cache/imgtdb_base.zip'
reference_igblast = pipelines_testdata_base_path + 'airrflow/database-cache/igblast_base.zip'

}

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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -81,8 +81,8 @@ params {
// -----------------------
productive_only = true
reassign = true
reference_igblast = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip'
reference_fasta = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip'
reference_igblast = "${params.pipelines_testdata_base_path}airrflow/database-cache/igblast_base.zip"
reference_fasta = "${pipelines_testdata_base_path}airrflow/database-cache/imgtdb_base.zip"
fetch_imgt = false
save_databases = true
isotype_column = 'c_call'
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