Merge pull request #639 from jfy133/circularmapper-filter-fix

Circularmapper filter fix

Author: jfy133

CHANGELOG.md

@@ -14,7 +14,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - Removed leftover old DockerHub push CI commands.
 - [#627](https://github.com/nf-core/eager/issues/627) - Added de Barros Damgaard citation to README
 - [#630](https://github.com/nf-core/eager/pull/630) - Better handling of Qualimap memory requirements and error strategy.
-- Fixed some imcomplete schema options to ensure users supply valid input values
+- Fixed some incomplete schema options to ensure users supply valid input values
+- [#638](https://github.com/nf-core/eager/issues/638#issuecomment-748877567) Fixed inverted circularfilter filtering (previously filtering would happen by default, not when requested by user as originally recorded in documentation)
 
 ### `Dependencies`
 

main.nf

@@ -87,7 +87,7 @@ def helpMessage() {
       --bwaalnl [num]            Specify the -l parameter for BWA aln, i.e. length of seeds to be used. Set to 1024 for whole read. Default: ${params.bwaalnl}
       --circularextension [num]  Specify the number of bases to extend reference by (circularmapper only). Default: ${params.circularextension}
       --circulartarget [chr]     Specify the FASTA header of the target chromosome to extend(circularmapper only). Default: '${params.circulartarget}'
-      --circularfilter [bool]    Turn on to filter off-target reads (circularmapper only).
+      --circularfilter [bool]    Turn on to remove reads that did not map to the circularised genome (circularmapper only).
       --bt2_alignmode [str]      Specify the bowtie2 alignment mode. Options:  'local', 'end-to-end'. Default: '${params.bt2_alignmode}'
       --bt2_sensitivity [str]    Specify the level of sensitivity for the bowtie2 alignment mode. Options: 'no-preset', 'very-fast', 'fast', 'sensitive', 'very-sensitive'. Default: '${params.bt2_sensitivity}'
       --bt2n [num]               Specify the -N parameter for bowtie2 (mismatches in seed). This will override defaults from alignmode/sensitivity. Default: ${params.bt2n}
@@ -1549,6 +1549,7 @@ process circulargenerator{
             else null
     }
 
+
     input:
     file fasta from ch_fasta_for_circulargenerator
 
@@ -1586,7 +1587,7 @@ process circularmapper{
     params.mapper == 'circularmapper'
 
     script:
-    def filter = params.circularfilter ? '' : '-f true -x false'
+    def filter = params.circularfilter ? '-f true -x true' : ''
     def elongated_root = "${fasta.baseName}_${params.circularextension}.fasta"
     def size = params.large_ref ? '-c' : ''
 

nextflow_schema.json

@@ -555,9 +555,9 @@
                 },
                 "circularfilter": {
                     "type": "boolean",
-                    "description": "Turn on to filter off-target reads (circularmapper only).",
+                    "description": "Turn on to remove reads that did not map to the circularised genome (circularmapper only).",
                     "fa_icon": "fas fa-filter",
-                    "help_text": "If you want to filter out reads that don't map to a circular chromosome, turn this on. By default this option is turned off.\n"
+                    "help_text": "If you want to filter out reads that don't map to a circular chromosome (and also non-circular chromosome headers) from the resulting BAM file, turn this on. By default this option is turned off.\n> Modifies -f and -x parameters of CircularMapper's realignsamfile\n"
                 },
                 "bt2_alignmode": {
                     "type": "string",
@@ -1601,4 +1601,4 @@
             "$ref": "#/definitions/metagenomic_authentication"
         }
     ]
-}
+}