Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

parameterize more assembly knobs #457

Merged
merged 5 commits into from
Mar 8, 2023
Merged

parameterize more assembly knobs #457

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
38cad1c
parameterize
dpark01 Feb 24, 2023
a8ad05e
typo
dpark01 Feb 24, 2023
3723eeb
allow user to override assemble_refbased aligner and aligner params
dpark01 Mar 7, 2023
be0e257
Merge branch 'master' into dp-coverage
dpark01 Mar 7, 2023
6afa2e5
Merge branch 'master' into dp-coverage
dpark01 Mar 7, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 3 additions & 3 deletions pipes/WDL/workflows/assemble_refbased.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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 {
Expand Down
4 changes: 2 additions & 2 deletions pipes/WDL/workflows/sarscov2_illumina_full.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -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

Expand Down Expand Up @@ -121,11 +122,10 @@ 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,
min_coverage = 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
Expand Down