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

Jump to bottom

classify_single: parameterize taxa to deplete #536

Merged
merged 4 commits into from
May 3, 2024
Merged

classify_single: parameterize taxa to deplete #536

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
fedae7a
bugfix for exposing optional param for WDL 1.1 interp of optionals
dpark01 May 3, 2024
1e7b286
rename new inputs to be consistent with the metagenomic_denovo workflow
dpark01 May 3, 2024
65dea0d
push in an old parameterization
dpark01 May 3, 2024
4813728
attempt to fix build errors
dpark01 May 3, 2024
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
12 changes: 6 additions & 6 deletions pipes/WDL/tasks/tasks_16S_amplicon.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ task qiime_import_from_bam {
Int memory_mb = 7000
Int cpu = 5
Int disk_size_gb = ceil(2*20) + 5
String docker = "quay.io/broadinstitute/qiime2"
String docker = "quay.io/broadinstitute/qiime2:latest"
}
parameter_meta {
reads_bam: {
Expand Down Expand Up @@ -86,7 +86,7 @@ task trim_reads {
Int memory_mb = 2000
Int cpu = 4
Int disk_size_gb = ceil(2*size(reads_qza, "GiB")) + 5
String docker = "quay.io/broadinstitute/qiime2"
String docker = "quay.io/broadinstitute/qiime2:latest"
}
parameter_meta {
reads_qza: {
Expand Down Expand Up @@ -160,7 +160,7 @@ task join_paired_ends {
Int memory_mb = 2000
Int cpu = 1
Int disk_size_gb = ceil(2*size(trimmed_reads_qza, "GiB")) + 50
String docker = "quay.io/broadinstitute/qiime2"
String docker = "quay.io/broadinstitute/qiime2:latest"
}
parameter_meta{
trimmed_reads_qza: {
Expand Down Expand Up @@ -210,7 +210,7 @@ task deblur {
Int memory_mb = 2000
Int cpu = 1
Int disk_size_gb = ceil(2*size(joined_end_reads_qza, "GiB")) + 5
String docker = "quay.io/broadinstitute/qiime2"
String docker = "quay.io/broadinstitute/qiime2:latest"
}
parameter_meta {
joined_end_reads_qza: {
Expand Down Expand Up @@ -288,7 +288,7 @@ task train_classifier {
Int memory_mb = 2000
Int cpu = 1
Int disk_size_gb = ceil(2*size(otu_ref, "GiB")) + 5
String docker = "quay.io/broadinstitute/qiime2"
String docker = "quay.io/broadinstitute/qiime2:latest"
}
parameter_meta{
otu_ref: {
Expand Down Expand Up @@ -372,7 +372,7 @@ task tax_analysis {
Int memory_mb = 5
Int cpu = 1
Int disk_size_gb = 375
String docker = "quay.io/broadinstitute/qiime2"
String docker = "quay.io/broadinstitute/qiime2:latest"
}
parameter_meta{
trained_classifier: {
Expand Down
6 changes: 3 additions & 3 deletions pipes/WDL/tasks/tasks_read_utils.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -173,10 +173,10 @@ task merge_and_reheader_bams {
String out_basename = basename(in_bams[0], ".bam")

String docker = "quay.io/broadinstitute/viral-core:2.3.1"
Int disk_size = 750
Int machine_mem_gb = 4
}

Int disk_size = 750

command <<<
set -ex -o pipefail

Expand Down Expand Up @@ -224,7 +224,7 @@ task merge_and_reheader_bams {

runtime {
docker: docker
memory: "3 GB"
memory: machine_mem_gb + " GB"
cpu: 2
disks: "local-disk " + disk_size + " LOCAL"
disk: disk_size + " GB" # TES
Expand Down
7 changes: 5 additions & 2 deletions pipes/WDL/workflows/classify_single.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,9 @@ workflow classify_single {

File kraken2_db_tgz
File krona_taxonomy_db_kraken2_tgz

Array[String] taxa_to_dehost = ["Vertebrata"]
Array[String] taxa_to_avoid_assembly = ["Vertebrata", "other sequences", "Bacteria"]
}

parameter_meta {
Expand Down Expand Up @@ -96,7 +99,7 @@ workflow classify_single {
classified_reads_txt_gz = kraken2.kraken2_reads_report,
ncbi_taxonomy_db_tgz = ncbi_taxdump_tgz,
exclude_taxa = true,
taxonomic_names = ["Vertebrata"],
taxonomic_names = taxa_to_dehost,
out_filename_suffix = "hs_depleted"
}
call reports.fastqc as fastqc_cleaned {
Expand All @@ -108,7 +111,7 @@ workflow classify_single {
classified_reads_txt_gz = kraken2.kraken2_reads_report,
ncbi_taxonomy_db_tgz = ncbi_taxdump_tgz,
exclude_taxa = true,
taxonomic_names = ["Vertebrata", "other sequences", "Bacteria"],
taxonomic_names = taxa_to_avoid_assembly,
out_filename_suffix = "acellular"
}
call read_utils.rmdup_ubam {
Expand Down