diff --git a/configs/example.config b/configs/example.config index c1f694ea..97004a32 100644 --- a/configs/example.config +++ b/configs/example.config @@ -47,7 +47,6 @@ //params.primer_bed = "Cecret/configs/artic_V3_nCoV-2019.bed" //params.amplicon_bed = "Cecret/configs/nCoV-2019.insert.bed" - //# Tool toggles //params.trimmer = 'ivar' //params.trimmer = 'samtools' @@ -120,6 +119,10 @@ iqtree_container = 'staphb/iqtree:latest' //params.samtools_coverage_options = '' //params.samtools_coverage = true +//# For process samtools_depth +//params.samtools_depth_options = '' +//params.samtools_depth = true + //# For process samtools_flagstat //params.samtools_flagstat_options = '' //params.samtools_flagstat = true @@ -138,7 +141,7 @@ iqtree_container = 'staphb/iqtree:latest' //params.samtools_ampliconstats_options = '' //params.samtools_ampliconstats = true -//# For process samtools_ampliconstats +//# For process samtools_plot_ampliconstats //params.samtools_plot_ampliconstats_options = '-size 1200,900 -size2 1200,900 -size3 1200,900' //params.samtools_plot_ampliconstats = true @@ -247,7 +250,7 @@ process { } withName:bamsnap{ - cpus = 'params.medpus' + cpus = 'params.medcpus' errorStrategy = 'ignore' container = bamsnap_container time = '1h' @@ -265,6 +268,10 @@ process { container = samtools_container } + withName:samtools_depth{ + container = samtools_container + } + withName:kraken2{ cpus = "params.maxcpus" container = kraken2_container @@ -287,14 +294,13 @@ process { container = pangolin_container } - withName:nextclade{ cpus = "params.maxcpus" container = nextclade_container } withName:vadr{ - cpus = 'params.medpus' + cpus = 'params.medcpus' memory = 'params.maxmem' container = 'staphb/vadr:latest' }