Skip to content

Commit

Permalink
setting vadr_skip_length via organism_parameters subworkflow as this … (
Browse files Browse the repository at this point in the history 
#418)

* setting vadr_skip_length via organism_parameters subworkflow as this is taxa-specific. not tested yet

* set vadr_skip_length via organism_parameters subworkflow - theiacov_illumina_pe and ont

* add optional input vadr_skip_length to theiacov_fasta and illumina_se

* theiacov_ont: added vadr_skip_length to org_param call block
  • Loading branch information
@kapsakcj
kapsakcj authored Apr 17, 2024
1 parent a8e0288 commit 2dff853
Show file tree
Hide file tree
Showing 5 changed files with 27 additions and 3 deletions.
7 changes: 5 additions & 2 deletions workflows/theiacov/wf_theiacov_fasta.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,8 @@ workflow theiacov_fasta {
# qc check parameters
File? qc_check_table
# vadr parameters
Int? max_length
Int? vadr_max_length
Int? vadr_skip_length
String? vadr_opts
Int? vadr_memory
}
Expand All @@ -55,7 +56,8 @@ workflow theiacov_fasta {
genome_length_input = genome_length,
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = max_length,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_opts,
vadr_mem = vadr_memory
}
Expand Down Expand Up @@ -96,6 +98,7 @@ workflow theiacov_fasta {
assembly_length_unambiguous = consensus_qc.number_ATCG,
max_length = organism_parameters.vadr_maxlength,
vadr_opts = organism_parameters.vadr_opts,
skip_length = organism_parameters.vadr_skiplength,
memory = organism_parameters.vadr_memory
}
}
Expand Down
5 changes: 5 additions & 0 deletions workflows/theiacov/wf_theiacov_illumina_pe.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ workflow theiacov_illumina_pe {
String? nextclade_dataset_name
# vadr parameters
Int? vadr_max_length
Int? vadr_skip_length
String? vadr_options
Int? vadr_memory
# read screen parameters
Expand Down Expand Up @@ -77,6 +78,7 @@ workflow theiacov_illumina_pe {
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_options,
primer_bed_file = primer_bed,
pangolin_docker_image = pangolin_docker_image,
Expand Down Expand Up @@ -186,6 +188,7 @@ workflow theiacov_illumina_pe {
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_options,
vadr_mem = vadr_memory,
primer_bed_file = primer_bed,
Expand All @@ -206,6 +209,7 @@ workflow theiacov_illumina_pe {
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_options,
primer_bed_file = primer_bed,
gene_locations_bed_file = reference_gene_locations_bed,
Expand Down Expand Up @@ -299,6 +303,7 @@ workflow theiacov_illumina_pe {
assembly_length_unambiguous = consensus_qc.number_ATCG,
vadr_opts = organism_parameters.vadr_opts,
max_length = organism_parameters.vadr_maxlength,
skip_length = organism_parameters.vadr_skiplength,
memory = organism_parameters.vadr_memory
}
}
Expand Down
3 changes: 3 additions & 0 deletions workflows/theiacov/wf_theiacov_illumina_se.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -52,6 +52,7 @@ workflow theiacov_illumina_se {
Boolean skip_mash = false
# vadr parameters
Int? vadr_max_length
Int? vadr_skip_length
String? vadr_options
Int? vadr_memory
# pangolin parameters
Expand All @@ -69,6 +70,7 @@ workflow theiacov_illumina_se {
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_options,
vadr_mem = vadr_memory,
primer_bed_file = primer_bed,
Expand Down Expand Up @@ -173,6 +175,7 @@ workflow theiacov_illumina_se {
assembly_length_unambiguous = consensus_qc.number_ATCG,
vadr_opts = organism_parameters.vadr_opts,
max_length = organism_parameters.vadr_maxlength,
skip_length = organism_parameters.vadr_skiplength,
memory = organism_parameters.vadr_memory
}
}
Expand Down
5 changes: 5 additions & 0 deletions workflows/theiacov/wf_theiacov_ont.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -53,6 +53,7 @@ workflow theiacov_ont {
Boolean skip_mash = false
# vadr parameters
Int? vadr_max_length
Int? vadr_skip_length
String? vadr_options
Int? vadr_memory
# pangolin parameters
Expand All @@ -69,6 +70,7 @@ workflow theiacov_ont {
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_options,
vadr_mem = vadr_memory,
primer_bed_file = primer_bed,
Expand Down Expand Up @@ -165,6 +167,7 @@ workflow theiacov_ont {
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_options,
primer_bed_file = primer_bed,
gene_locations_bed_file = reference_gene_locations_bed,
Expand All @@ -183,6 +186,7 @@ workflow theiacov_ont {
nextclade_dataset_tag_input = nextclade_dataset_tag,
nextclade_dataset_name_input = nextclade_dataset_name,
vadr_max_length = vadr_max_length,
vadr_skip_length = vadr_skip_length,
vadr_options = vadr_options,
primer_bed_file = primer_bed,
gene_locations_bed_file = reference_gene_locations_bed,
Expand Down Expand Up @@ -291,6 +295,7 @@ workflow theiacov_ont {
assembly_length_unambiguous = consensus_qc.number_ATCG,
vadr_opts = organism_parameters.vadr_opts,
max_length = organism_parameters.vadr_maxlength,
skip_length = organism_parameters.vadr_skiplength,
memory = organism_parameters.vadr_memory
}
}
Expand Down
10 changes: 9 additions & 1 deletion workflows/utilities/wf_organism_parameters.wdl
View file
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ workflow organism_parameters {

# vadr parameters
Int? vadr_max_length
Int? vadr_skip_length
String? vadr_options
Int? vadr_mem

Expand All @@ -45,6 +46,7 @@ workflow organism_parameters {
String sc2_pangolin_docker = "us-docker.pkg.dev/general-theiagen/staphb/pangolin:4.3.1-pdata-1.26"
Int sc2_genome_len = 29903
Int sc2_vadr_max_length = 30000
Int sc2_vadr_skip_length = 10000
String sc2_vadr_options = "--noseqnamemax --glsearch -s -r --nomisc --mkey sarscov2 --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn --out_allfasta"
Int sc2_vadr_memory = 8
}
Expand All @@ -59,6 +61,7 @@ workflow organism_parameters {
String mpox_reference_gff_file = "gs://theiagen-public-files/terra/mpxv-files/Mpox-MT903345.1.reference.gff3"
String mpox_vadr_options = "--glsearch -s -r --nomisc --mkey mpxv --r_lowsimok --r_lowsimxd 100 --r_lowsimxl 2000 --alt_pass discontn,dupregin --out_allfasta --minimap2 --s_overhang 150"
Int mpox_vadr_max_length = 210000
Int mpox_vadr_skip_length = 65480
Int mpox_vadr_memory = 8
Int mpox_genome_len = 197200
}
Expand All @@ -70,6 +73,7 @@ workflow organism_parameters {
Int wnv_genome_len = 11000
String wnv_vadr_options = "--mkey flavi --mdir /opt/vadr/vadr-models-flavi/ --nomisc --noprotid --out_allfasta"
Int wnv_vadr_max_length = 11000
Int wnv_vadr_skip_length = 3000
Int wnv_vadr_memory = 8
String wnv_nextclade_ds_tag = "NA"
String wnv_nextclade_ds_name = "NA"
Expand All @@ -78,9 +82,10 @@ workflow organism_parameters {
String flu_org_name = "flu"
Int flu_genome_len = 13500

# vadr options are dummy options for flu right now
# vadr options for flu
String flu_vadr_options = "--atgonly --xnocomp --nomisc --alt_fail extrant5,extrant3 --mkey flu"
Int flu_vadr_max_length = 13500
Int flu_vadr_skip_length = 500
Int flu_vadr_memory = 8

# setting nextclade parameters
Expand Down Expand Up @@ -137,6 +142,7 @@ workflow organism_parameters {
Int rsv_a_genome_len = 16000
String rsv_a_vadr_options = "-r --mkey rsv --xnocomp"
Int rsv_a_vadr_max_length = 15500
Int rsv_a_vadr_skip_length = 5000
Int rsv_a_vadr_memory = 32
}
if (organism == "rsv_b" || organism == "rsv-b" || organism == "RSV-B" || organism == "RSV_B") {
Expand All @@ -147,6 +153,7 @@ workflow organism_parameters {
Int rsv_b_genome_len = 16000
String rsv_b_vadr_options = "-r --mkey rsv --xnocomp"
Int rsv_b_vadr_max_length = 15500
Int rsv_b_vadr_skip_length = 5000
Int rsv_b_vadr_memory = 32
}
if (organism == "HIV" && hiv_primer_version == "v1") {
Expand Down Expand Up @@ -184,6 +191,7 @@ workflow organism_parameters {
String vadr_opts = select_first([vadr_options, sc2_vadr_options, mpox_vadr_options, wnv_vadr_options, flu_vadr_options, rsv_a_vadr_options, rsv_b_vadr_options, "NA"])
Int vadr_maxlength = select_first([vadr_max_length, sc2_vadr_max_length, mpox_vadr_max_length, wnv_vadr_max_length, flu_vadr_max_length, rsv_a_vadr_max_length, rsv_b_vadr_max_length, 0])
Int vadr_memory = select_first([vadr_mem, sc2_vadr_memory, mpox_vadr_memory, wnv_vadr_memory, flu_vadr_memory, rsv_a_vadr_memory, rsv_b_vadr_memory, 0])
Int vadr_skiplength = select_first([vadr_skip_length, sc2_vadr_skip_length, mpox_vadr_skip_length, wnv_vadr_skip_length, flu_vadr_skip_length, rsv_a_vadr_skip_length, rsv_b_vadr_skip_length, 0])
# kraken options
String kraken_target_organism = select_first([kraken_target_organism_input, mpox_kraken_target_organism, wnv_kraken_target_organism, hiv_v1_target_organism, hiv_v2_target_organism, ""])
}
Expand Down

0 comments on commit 2dff853

Please sign in to comment.