rm unnecessary isotype_column param

ggabernet · Nov 25, 2024 · a28675d · a28675d
1 parent 92fff0c
commit a28675d
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Showing 13 changed files with 0 additions and 19 deletions.
diff --git a/conf/clontech_umi_bcr.config b/conf/clontech_umi_bcr.config
@@ -38,5 +38,4 @@ params {
     primer_r1_maxerror = 0.2
     assemblepairs_sequential = true
     primer_consensus = 0.6
-    isotype_column = 'cregion'
 }
diff --git a/conf/nebnext_umi_bcr.config b/conf/nebnext_umi_bcr.config
@@ -35,5 +35,4 @@ params {
     cregion_maxlen = 100
     cregion_maxerror = 0.3
     cregion_mask_mode = 'tag'
-    isotype_column = 'cregion'
 }
diff --git a/conf/test.config b/conf/test.config
@@ -37,7 +37,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
     lineage_trees = true
 }
 

diff --git a/conf/test_fetchimgt.config b/conf/test_fetchimgt.config
@@ -35,7 +35,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
 }
 
 process{

diff --git a/conf/test_full.config b/conf/test_full.config
@@ -36,7 +36,6 @@ params {
     umi_length = 15
     umi_start = 0
     umi_position = 'R1'
-    isotype_column = 'c_primer'
 }
 
 process {

diff --git a/conf/test_maskprimers_align.config b/conf/test_maskprimers_align.config
@@ -36,6 +36,5 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
     maskprimers_align = true
 }
diff --git a/conf/test_maskprimers_extract.config b/conf/test_maskprimers_extract.config
@@ -35,7 +35,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
     lineage_trees = false
     primer_r1_mask_mode = 'trim'
     primer_r2_mask_mode = 'cut'

diff --git a/conf/test_no_umi.config b/conf/test_no_umi.config
@@ -26,7 +26,6 @@ params {
     vprimer_start = 4
     primer_revpr = true
     umi_length = 0
-    isotype_column = 'c_primer'
 
     // Input data
     input = pipelines_testdata_base_path + 'testdata-no-umi/Metadata_test-no-umi_airr.tsv'

diff --git a/conf/test_nocluster.config b/conf/test_nocluster.config
@@ -38,7 +38,6 @@ params {
     cluster_sets = false
     index_file = true
     clonal_threshold = 0.15
-    isotype_column = 'c_primer'
 }
 
 process{

diff --git a/conf/test_raw_immcantation_devel.config b/conf/test_raw_immcantation_devel.config
@@ -37,7 +37,6 @@ params {
     umi_start = 6
     umi_position = 'R1'
     index_file = true
-    isotype_column = 'c_primer'
 }
 
 process{

diff --git a/modules/local/enchantr/define_clones.nf b/modules/local/enchantr/define_clones.nf
@@ -59,7 +59,6 @@ process DEFINE_CLONES {
                                         'threshold'=${thr}, \\
                                         'singlecell'='${params.singlecell}', \\
                                         'outdir'=getwd(), \\
-                                        'isotype_column'='${params.isotype_column}', \\
                                         'nproc'=${task.cpus}, \\
                                         'log'='${meta.id}_clone_command_log' ${args}))"
 

diff --git a/nextflow.config b/nextflow.config
@@ -88,7 +88,6 @@ params {
     reference_fasta = "${params.pipelines_testdata_base_path}database-cache/imgtdb_base.zip"
     fetch_imgt = false
     save_databases = true
-    isotype_column = 'c_call'
     skip_alignment_filter = false
 
     // -----------------------

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -395,13 +395,6 @@
                     "type": "boolean",
                     "description": "Set this flag to fetch the IMGT reference data at runtime.",
                     "fa_icon": "fas fa-cloud-download-alt"
-                },
-                "isotype_column": {
-                    "type": "string",
-                    "description": "Set the column in the AIRR rearrangement file that isotype information should be gathered from.",
-                    "default": "c_call",
-                    "fa_icon": "fas fa-border-all",
-                    "help_text": "Default is the `c_call` column. For bulk protocols one can use the c_primers or cregion columns (check `align_cregion`). The primer or cregions fasta file header need to contain the strings `IGHA`, `IGHD`, `IGHG`... for the isotypes to be properly parsed. This will be used for plotting mutation frequency by isotype in the clonal analysis report."
                 }
             },
             "fa_icon": "fas fa-edit"