Merge pull request #892 from nf-core/patch-testconfig_params_updates

Remove deprecated params from benchmarking profiles

Author: jfy133

CHANGELOG.md

@@ -13,6 +13,8 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#879](https://github.com/nf-core/eager/issues/879) Add missing threads parameter for pre-clipping FastQC for single end data that caused insufficient memory in some cases (♥ to @marcel-keller for reporting)
 - [#885](https://github.com/nf-core/eager/issues/885) Specify task memory for all tools in get_software_versions to account for incompatibilty of java with some SGE clusters causing hanging of the process (♥ to @maxibor for reporting)
 - [#887](https://github.com/nf-core/eager/issues/887) Clarify what is considered 'ultra-short' reads in the help text of clip_readlength, for when you may wish to turn of length filtering during AdapterRemoval (♥ to @TCLamnidis for reporting)
+- [#889](https://github.com/nf-core/eager/issues/889) Remove/updated parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting)
+
 
 ### `Dependencies`
 

conf/benchmarking_human.config

@@ -12,26 +12,24 @@ params {
    config_profile_description = "A 'fullsized' benchmarking profile for deepish Human sequencing aDNA data" 
 
    //Input data
-   input = 'https://raw.githubusercontent.com/jfy133/test-datasets/eager/testdata/Benchmarking/benchmarking_human.tsv'
+   input = 'https://raw.githubusercontent.com/nf-core/test-datasets/eager/testdata/Benchmarking/benchmarking_human.tsv'
    // Genome reference
    fasta = 'https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz'
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 30
 
    dedupper = 'markduplicates'
 
    run_trim_bam = true
-   bamutils_clip_left = 1
-   bamutils_clip_right = 1
+   bamutils_clip_double_stranded_none_udg_left = 1
+   bamutils_clip_double_stranded_none_udg_right = 1
 
    // JAR will need to be downloaded first!
    run_genotyping = true
    genotyping_tool = 'ug'
    genotyping_source = 'trimmed'
-   gatk_ug_jar = 'GenomeAnalysisTK.jar'
    gatk_call_conf = 20
 
    run_sexdeterrmine = true
@@ -41,8 +39,6 @@ params {
    contamination_chrom_name = 'chrX'
 
    run_mtnucratio = true
-
-
 }
 
 process {

conf/benchmarking_vikingfish.config

@@ -20,7 +20,6 @@ params {
    bwaalnl = 1024
 
    run_bam_filtering = true
-   bam_discard_unmapped = true
    bam_unmapped_type = 'discard'
    bam_mapping_quality_threshold = 25