rm comments / TODOs

nf-core · Mar 14, 2023 · 652baeb · 652baeb
1 parent 4bfb956
commit 652baeb
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diff --git a/nextflow.config b/nextflow.config
@@ -86,11 +86,6 @@ params {
     igphyml="/usr/local/bin/igphyml"
     skip_lineage = false
 
-
-    // old bcellmagic options ----------------------
-    // Clustering parameters
-    // threshold_method = 'density'
-
     // -----------------------
     // reporting options
     // -----------------------

diff --git a/subworkflows/local/assembled_input_check.nf b/subworkflows/local/assembled_input_check.nf
@@ -10,7 +10,6 @@ workflow ASSEMBLED_INPUT_CHECK {
     miairr
     collapseby
     cloneby
-    //reassign
 
     main:
     // TODO: validate input should check that sample_ids are unique

diff --git a/workflows/airrflow.nf b/workflows/airrflow.nf
@@ -9,7 +9,6 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
 // Validate input parameters
 WorkflowAirrflow.initialise(params, log)
 
-// TODO nf-core: Add all file path parameters for the pipeline to the list below
 // Check input path parameters to see if they exist
 def checkPathParamList = [ params.input, params.multiqc_config ]
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
@@ -45,7 +44,6 @@ ch_report_logo_img = Channel.fromPath(params.report_logo_img, checkIfExists: tru
 
 include { CHANGEO_CONVERTDB_FASTA as CHANGEO_CONVERTDB_FASTA_FROM_AIRR } from '../modules/local/changeo/changeo_convertdb_fasta'
 
-
 //
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
-Original file line number
+Diff line change
@@ Expand Up / @@ -10,7 +10,6 @@ workflow ASSEMBLED_INPUT_CHECK { @@
         miairr
         collapseby
         cloneby
-        //reassign
         main:
         // TODO: validate input should check that sample_ids are unique
@@ Expand Down @@