Add parameter for turning on longread host removal

conf/test.config

@@ -28,7 +28,7 @@ params {
     perform_longread_clip                 = false
     perform_shortread_complexityfilter    = true
     perform_shortread_hostremoval         = true
-    shortread_hostremoval_reference       = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/genome/genome.fasta'
+    perform_longread_hostremoval          = true
     run_kaiju                             = true
     run_kraken2                           = true
     run_malt                              = true

docs/usage.md

@@ -191,7 +191,7 @@ You can optionally save the FASTQ output of the run merging with the `--save_com
 
 #### Host Removal
 
-Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval`
+Removal of possible-host reads from FASTQ files prior profiling can be activated with `--perform_shortread_hostremoval` or `--perform_longread_hostremoval`.
 
 Similarly to complexity filtering, host-removal can be useful for runtime optimisation and reduction in misclassified reads. It is not always necessary to report classification of reads from a host when you already know the host of the sample, therefore you can gain a run-time and computational advantage by removing these prior typically resource-heavy profiling with more efficient methods. Furthermore, particularly with human samples, you can reduce the number of false positives during profiling that occur due to host-sequence contamination in reference genomes on public databases.
 

nextflow.config

@@ -82,7 +82,7 @@ params {
 
     // Host Removal
     perform_shortread_hostremoval          = false
-    shortread_hostremoval_reference        = null
+    perform_longread_hostremoval           = false
     shortread_hostremoval_index            = null
     longread_hostremoval_index             = null
     save_hostremoval_index                 = false

nextflow_schema.json

@@ -362,7 +362,9 @@
         "perform_shortread_hostremoval": {
             "type": "boolean"
         },
-        "shortread_hostremoval_reference": {
+        "perform_longread_hostremoval": {
+            "type": "boolean"
+        },
             "type": "string",
             "default": "None"
         },