From 951433dedadc9b4904b1a476bb114526b2b8a968 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Mon, 30 May 2022 20:16:00 +0200 Subject: [PATCH 1/2] Remove deprecated params from benchmarking profiles --- CHANGELOG.md | 1 + conf/benchmarking_human.config | 10 +++------- conf/benchmarking_vikingfish.config | 1 - 3 files changed, 4 insertions(+), 8 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index a9a23c86b..2d469226b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian) - [#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) +- [#889](https://github.com/nf-core/eager/issues/889) Remove/update deprecated parameters from benchmarking test profiles (♥ to @TCLamnidis for reporting) ### `Dependencies` diff --git a/conf/benchmarking_human.config b/conf/benchmarking_human.config index dcd4a55ec..b8cbce224 100644 --- a/conf/benchmarking_human.config +++ b/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 { diff --git a/conf/benchmarking_vikingfish.config b/conf/benchmarking_vikingfish.config index 765cf1f4d..b7ec39b56 100644 --- a/conf/benchmarking_vikingfish.config +++ b/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 From d6cafa829ecd93c00a755aae53ba3b1339600d63 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Thu, 2 Jun 2022 12:58:34 +0200 Subject: [PATCH 2/2] Changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2d469226b..101ff9c2e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,7 +11,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. - [#882](https://github.com/nf-core/eager/pull/882) Define DSL1 execution explicitly, as new versions Nextflow made DSL2 default (♥ to & fix from @Lehmann-Fabian) - [#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) -- [#889](https://github.com/nf-core/eager/issues/889) Remove/update deprecated parameters from benchmarking test profiles (♥ 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`