From 38cad1c4a4cf6c582aaf74eca1fda4ff3d8b994b Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 24 Feb 2023 16:30:40 -0500 Subject: [PATCH 1/3] parameterize --- pipes/WDL/workflows/sarscov2_illumina_full.wdl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/pipes/WDL/workflows/sarscov2_illumina_full.wdl b/pipes/WDL/workflows/sarscov2_illumina_full.wdl index b687d38c4..a2fe7a64e 100644 --- a/pipes/WDL/workflows/sarscov2_illumina_full.wdl +++ b/pipes/WDL/workflows/sarscov2_illumina_full.wdl @@ -51,6 +51,7 @@ workflow sarscov2_illumina_full { Int min_genome_bases = 24000 Int max_vadr_alerts = 0 Int ntc_max_unambig = 3000 + Int? min_genome_coverage File? sample_rename_map @@ -125,7 +126,7 @@ workflow sarscov2_illumina_full { skip_mark_dupes = ampseq, trim_coords_bed = bed_rename.outfile, major_cutoff = 0.75, - min_coverage = if ampseq then 50 else 3 + min_coverage = if defined(min_genome_coverage) then min_coverage else (if ampseq then 50 else 3) } # log controls From a8ad05e6c1596df5f331ee2d333adcecf196b681 Mon Sep 17 00:00:00 2001 From: Daniel Park Date: Fri, 24 Feb 2023 16:33:16 -0500 Subject: [PATCH 2/3] typo --- pipes/WDL/workflows/sarscov2_illumina_full.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pipes/WDL/workflows/sarscov2_illumina_full.wdl b/pipes/WDL/workflows/sarscov2_illumina_full.wdl index a2fe7a64e..c62a3e40d 100644 --- a/pipes/WDL/workflows/sarscov2_illumina_full.wdl +++ b/pipes/WDL/workflows/sarscov2_illumina_full.wdl @@ -126,7 +126,7 @@ workflow sarscov2_illumina_full { skip_mark_dupes = ampseq, trim_coords_bed = bed_rename.outfile, major_cutoff = 0.75, - min_coverage = if defined(min_genome_coverage) then min_coverage else (if ampseq then 50 else 3) + min_coverage = if defined(min_genome_coverage) then min_genome_coverage else (if ampseq then 50 else 3) } # log controls From 3723eeb04c2d965f6e71f9e2b30cee01c704bf2b Mon Sep 17 00:00:00 2001 From: Danny Park Date: Tue, 7 Mar 2023 09:15:45 -0500 Subject: [PATCH 3/3] allow user to override assemble_refbased aligner and aligner params --- pipes/WDL/workflows/assemble_refbased.wdl | 6 +++--- pipes/WDL/workflows/sarscov2_illumina_full.wdl | 1 - 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/pipes/WDL/workflows/assemble_refbased.wdl b/pipes/WDL/workflows/assemble_refbased.wdl index 3001f9dfb..f624252e4 100644 --- a/pipes/WDL/workflows/assemble_refbased.wdl +++ b/pipes/WDL/workflows/assemble_refbased.wdl @@ -67,18 +67,18 @@ workflow assemble_refbased { Float major_cutoff=0.75 Boolean skip_mark_dupes=false File? trim_coords_bed - } - Map[String,String] align_to_ref_options = { + Map[String,String] align_to_ref_options = { "novoalign": "-r Random -l 40 -g 40 -x 20 -t 501 -k", "bwa": "-k 12 -B 1", "minimap2": "" } - Map[String,String] align_to_self_options = { + Map[String,String] align_to_self_options = { "novoalign": "-r Random -l 40 -g 40 -x 20 -t 100", "bwa": "", "minimap2": "" } + } scatter(reads_unmapped_bam in reads_unmapped_bams) { call assembly.align_reads as align_to_ref { diff --git a/pipes/WDL/workflows/sarscov2_illumina_full.wdl b/pipes/WDL/workflows/sarscov2_illumina_full.wdl index c62a3e40d..0c13d0d18 100644 --- a/pipes/WDL/workflows/sarscov2_illumina_full.wdl +++ b/pipes/WDL/workflows/sarscov2_illumina_full.wdl @@ -122,7 +122,6 @@ workflow sarscov2_illumina_full { reads_unmapped_bams = name_reads.right, reference_fasta = reference_fasta, sample_name = name_reads.left, - aligner = "minimap2", skip_mark_dupes = ampseq, trim_coords_bed = bed_rename.outfile, major_cutoff = 0.75,