Merge pull request #327 from ggabernet/dev

Revert changes test_full

conf/test_full.config

@@ -9,16 +9,45 @@
 
 ----------------------------------------------------------------------------------------
 */
-includeConfig 'nebnext_umi_bcr.config'
 
 params {
     config_profile_name        = 'Full test profile'
     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'
+    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']
+
+    }
 }