Skip to content

Fix pycloneevi #11766

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

Merged
valerianilucrezia merged 6 commits into from
May 27, 2026
Merged

Fix pycloneevi #11766

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
7020bca
Remove space to trigger test
SPPearce May 26, 2026
95cc7f0
Update snapshot
SPPearce May 27, 2026
2c55144
Add .yaml
SPPearce May 27, 2026
3da8130
Merge branch 'master' into pyclonevi_check
SPPearce May 27, 2026
bee30ca
Update python script version extraction
SPPearce May 27, 2026
3164f23
Merge branch 'master' into pyclonevi_check
valerianilucrezia May 27, 2026
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
1 change: 0 additions & 1 deletion modules/nf-core/pyclonevi/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,6 @@ process PYCLONEVI {

stub:
def prefix = task.ext.prefix ?: "${meta.id}"

"""
touch ${prefix}_cluster_table.csv
touch ${prefix}.tsv
Expand Down
4 changes: 1 addition & 3 deletions modules/nf-core/pyclonevi/templates/main_script.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -163,9 +163,7 @@ def pyclone_ctree(joint, best_fit, ctree_input):

# Version
version = (
subprocess.check_output("pip show pyclone-vi | grep Version | awk '{print \$NF}'", shell=True)
.decode()
.split("\\n")[0]
subprocess.check_output("pyclone-vi --version | sed 's/.*version //g'", shell=True).decode().split("\\n")[0]
)

f = open("versions.yml", "a")
Expand Down
8 changes: 4 additions & 4 deletions modules/nf-core/pyclonevi/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,10 @@ nextflow_process {
assert process.success
assertAll(
{ assert snapshot(
sanitizeOutput(
process.out,
unstableKeys: ["ctree_input", "pyclone_input", "pyclone_all_fits", "pyclone_best_fit"]
)).match() }
sanitizeOutput(process.out,
unstableKeys: ["ctree_input", "pyclone_input", "pyclone_all_fits", "pyclone_best_fit"]),
path(process.out.versions_pyclonevi[0]).yaml
).match() }
)
}

Expand Down
19 changes: 12 additions & 7 deletions modules/nf-core/pyclonevi/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -43,19 +43,19 @@
]
],
"versions_pyclonevi": [
"versions.yml:md5,d7a72f90b5e871ad593d6b02ac78abb4"
"versions.yml:md5,bc0f9ae69eb48d45a2c7389d55f7882e"
]
},
{
"PYCLONEVI": {
"pyclonevi": "0.1.6"
"pyclonevi": "0.2.0"
}
}
],
"timestamp": "2026-05-26T11:01:04.192976421",
"timestamp": "2026-05-26T17:22:45.350487609",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
"nextflow": "26.04.2"
}
},
"pyclonevi": {
Expand Down Expand Up @@ -105,14 +105,19 @@
]
],
"versions_pyclonevi": [
"versions.yml:md5,764c065f67a1502d5158a8a018d8a388"
"versions.yml:md5,3d517410bfd758e0eea9bef7f40d22e6"
]
},
{
"PYCLONEVI": {
"pyclonevi": "0.2.0"
}
}
],
"timestamp": "2026-05-26T11:00:56.527463061",
"timestamp": "2026-05-27T07:54:19.275868186",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
"nextflow": "26.04.2"
}
}
}