Merge pull request #840 from nf-core/test-full-fix

Remove deprecated parameters from test profiles

Author: apeltzer

CHANGELOG.md

@@ -9,7 +9,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
-- [#838] Fix --snpcapture_bed files not being picked up by Nextflow
+- [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
+- [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow
 - Fix PMDtools reference mask not being picked up by Nextflow, and it's use being evaluated against --snpcapture_bed rather than --pmdtools_reference_mask
 - Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly. 
 

conf/test_full.config

@@ -21,7 +21,6 @@ params {
    bwaalnl = 1024
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 25
 

conf/test_stresstest_human.config

@@ -24,7 +24,6 @@ params {
    mtnucratio_header = 'ChrM'
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 30