removed --noYacrd, added --removeChimeras instead. Now default is not…

… to remove chimeras

README.md

@@ -213,6 +213,7 @@ Process specific parameters:
 
 Other control options:
     --isDemultiplexed             Set this flag to avoid Demultiplex sub-workflow. If set, each fastq file is
+    --removeChimeras              Set this flag to activate the chimera-removing step with Yacrd.
                                   processed as a different barcode.
     --noNanoplot                  Set this flag to avoid QCheck sub-workflow.
     --noSpeciesPolishing          Avoid the polishing sub-workflow.

main.nf

@@ -16,7 +16,7 @@ params.nanofilt_headcrop = 0
 params.nanofilt_tailcrop = 0
 params.yacrd_c = 4
 params.yacrd_n = 0.4
-params.noYacrd = false
+params.removeChimeras = false
 params.megan_lcaAlgorithm = "naive"
 params.megan_lcaCoveragePercent = 100
 params.megan_topPercent = 10
@@ -63,7 +63,7 @@ def parameters_expected = [
   'nanofilt_tailcrop',
   'yacrd_c',
   'yacrd_n',
-  'noYacrd', 'no-yacrd',
+  'removeChimeras', 'remove-chimeras',
   'megan_lcaAlgorithm', 'megan_lca-algorithm',
   'megan_lcaCoveragePercent', 'megan_lca-coverage-percent',
   'megan_topPercent', 'megan_top-percent',
@@ -309,7 +309,7 @@ def helpMessage() {
     Other control options:
         --isDemultiplexed             Set this flag to avoid Demultiplex sub-workflow. If set, each fastq file is 
                                       processed as a different barcode.
-        --noYacrd                     Set this flag to avoid chimera-removing step with Yacrd.
+        --removeChimeras              Set this flag to activate the chimera-removing step with Yacrd.
         --noNanoplot                  Set this flag to avoid QCheck sub-workflow. 
         --noSpeciesPolishing          Avoid the polishing sub-workflow.
         --lowAbundanceThreshold       The threshold of total abundance (counts) to be considered as "low", and

workflows/QFiltWorkflow.nf

@@ -10,7 +10,7 @@ workflow QFilt {
 
     main:
         NanoFilt( barcode_ch )
-        if (!params.noYacrd){
+        if (params.removeChimeras){
             AutoMap( NanoFilt.out )
             Yacrd( AutoMap.out )
             Yacrd.out