Skip to content

Update blastn module #8765

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

Open
wants to merge 6 commits into
base: master
Choose a base branch
from
+21 −4
Open

Update blastn module #8765

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
b524549
add taxid input and update test
AnnaNoren Jul 10, 2025
b25da4e
Add -taxids argument and input
AnnaNoren Aug 4, 2025
8c06830
add all taxid inputs and update test+snapshot
AnnaNoren Aug 6, 2025
8ed3421
Merge branch 'master' into add_taxidlist
LilyAnderssonLee Aug 15, 2025
604e36a
replace negative_taxidlist and negative_taxids inputs with boolean ne…
AnnaNoren Aug 19, 2025
0a63d97
Merge branch 'add_taxidlist' of github.com:AnnaNoren/modules into add…
AnnaNoren Aug 20, 2025
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
11 changes: 11 additions & 0 deletions modules/nf-core/blast/blastn/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,9 @@ process BLAST_BLASTN {
input:
tuple val(meta) , path(fasta)
tuple val(meta2), path(db)
path taxidlist
val taxids
val negative_tax

output:
tuple val(meta), path('*.txt'), emit: txt
Expand All @@ -23,6 +26,12 @@ process BLAST_BLASTN {
def prefix = task.ext.prefix ?: "${meta.id}"
def is_compressed = fasta.getExtension() == "gz" ? true : false
def fasta_name = is_compressed ? fasta.getBaseName() : fasta
def negative_tax_cmd = negative_tax ? "negative_" : ""
def taxidlist_cmd = taxidlist ? "-${negative_tax_cmd}taxidlist ${taxidlist}" : ""
def taxids_cmd = taxids ? "-${negative_tax_cmd}taxids ${taxids}" : ""
if (taxidlist_cmd.any() && taxids_cmd.any()) {
log.error("ERROR: taxidlist and taxids can not be used at the same time, choose only one argument to use for tax id filtering.")
Copy link
Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@muffato I added an if statement per your suggestion, similar to in the hifiasm module. However, It feels somewhat unnecessary because of how blast already outputs quite clear errors when using the two incompatible flags simultaneously. Hence, both the if statement will tell you, and blast errors will tell you. Whats your input, should the if statement stay or is it repetitive?

}

"""
if [ "${is_compressed}" == "true" ]; then
Expand All @@ -39,6 +48,8 @@ process BLAST_BLASTN {
-num_threads ${task.cpus} \\
-db \$DB \\
-query ${fasta_name} \\
${taxidlist_cmd} \\
${taxids_cmd} \\
${args} \\
-out ${prefix}.txt

Expand Down
6 changes: 6 additions & 0 deletions modules/nf-core/blast/blastn/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,9 @@ nextflow_process {
"""
input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]
input[1] = BLAST_MAKEBLASTDB.out.db
input[2] = []
input[3] = []
input[4] = []
"""
}
}
Expand All @@ -55,6 +58,9 @@ nextflow_process {
"""
input[0] = [ [id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) ]
input[1] = BLAST_MAKEBLASTDB.out.db
input[2] = []
input[3] = []
input[4] = []
"""
}
}
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/blast/blastn/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,9 @@
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "24.10.6"
},
"timestamp": "2025-04-01T11:32:43.169365323"
"timestamp": "2025-08-04T14:26:27.847166"
},
"versions_zipped": {
"content": [
Expand All @@ -19,8 +19,8 @@
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nextflow": "24.10.6"
},
"timestamp": "2025-04-01T11:32:48.452742327"
"timestamp": "2025-08-04T14:52:40.954652"
}
}