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

Test dev #616

Draft
wants to merge 3 commits into
base: dev
Choose a base branch
from
Draft

Test dev #616

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
10628e0
update container fusionreport
rannick Jan 20, 2025
2c59f51
fix path to process
rannick Jan 22, 2025
9b6cd24
Merge branch 'dev' into test-dev
rannick Feb 3, 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
2 changes: 1 addition & 1 deletion conf/modules.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -360,7 +360,7 @@ process {
]
}

withName: 'NFCORE_RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
withName: 'NFCORE_RNAFUSION:RNAFUSION:BUILD_REFERENCES:STARFUSION_BUILD' {
cpus = { 24 * task.attempt }
memory = { 100.GB * task.attempt }
time = { 2.d * task.attempt }
Expand Down
4 changes: 2 additions & 2 deletions subworkflows/local/fusioncatcher_workflow/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ workflow FUSIONCATCHER_WORKFLOW {
take:
reads // channel [ meta, [ fastqs ] ]
fusioncatcher_ref // channel [ meta, path ]
run_fusioncatcher // boolean
fusioncatcher // boolean
all // boolean
fusioninspector_only // boolean
fusioncatcher_fusions // path, string
Expand All @@ -18,7 +18,7 @@ workflow FUSIONCATCHER_WORKFLOW {
ch_versions = Channel.empty()
ch_dummy_file = file("$baseDir/assets/dummy_file_fusioncatcher.txt", checkIfExists: true)

if (( run_fusioncatcher || all) && !fusioninspector_only ) {
if (( fusioncatcher || all) && !fusioninspector_only ) {
if (fusioncatcher_fusions){

ch_fusioncatcher_fusions = reads.combine(Channel.value(file(fusioncatcher_fusions, checkIfExists:true)))
Expand Down
2 changes: 1 addition & 1 deletion workflows/rnafusion.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -122,7 +122,7 @@ workflow RNAFUSION {
FUSIONCATCHER_WORKFLOW (
ch_reads,
BUILD_REFERENCES.out.ch_fusioncatcher_ref, // channel [ meta, path ]
params.run_fusioncatcher,
params.fusioncatcher,
params.all,
params.fusioninspector_only,
params.fusioncatcher_fusions
Expand Down
Loading