From 40038918cbb341ffae630bec2d98b997377d74b4 Mon Sep 17 00:00:00 2001 From: Gisela Gabernet Date: Mon, 22 Apr 2024 18:32:07 -0400 Subject: [PATCH] revert changes test full --- conf/test_full.config | 31 ++++++++++++++++++++++++++++++- 1 file changed, 30 insertions(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 75b8b7b9..67d37c0b 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -9,7 +9,6 @@ ---------------------------------------------------------------------------------------- */ -includeConfig 'nebnext_umi_bcr.config' params { config_profile_name = 'Full test profile' @@ -17,8 +16,38 @@ params { // Input data input = 'https://raw.githubusercontent.com/nf-core/test-datasets/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' imgtdb_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/imgtdb_base.zip' igblast_base = 'https://raw.githubusercontent.com/nf-core/test-datasets/airrflow/database-cache/igblast_base.zip' lineage_trees = true + + // Other params + library_generation_method = 'specific_pcr_umi' + cprimer_position = 'R1' + umi_length = 15 + umi_start = 0 + umi_position = 'R1' +} + +process { + withName:DOWSER_LINEAGES{ + ext.args = ['minseq':5, + 'traits':'isotype', + 'tips':'isotype'] + } + + withName:DEFINE_CLONES_COMPUTE{ + ext.args = ['outname':'', 'model':'hierarchical', + 'method':'nt', 'linkage':'single', + 'min_n':30, 'isotype_column':'c_primer'] + + } + withName:DEFINE_CLONES_REPORT{ + ext.args = ['outname':'', 'model':'hierarchical', + 'method':'nt', 'linkage':'single', + 'min_n':30, 'isotype_column':'c_primer'] + + } }