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

fixes sample fastq output bug in cellranger mkfastq #6190

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
+3 −3
Open

fixes sample fastq output bug in cellranger mkfastq #6190

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
75fab2f
expand subdir search to capture fastq outputs
julicudini Aug 14, 2024
5e04b45
Merge branch 'nf-core:master' into master
julicudini Aug 15, 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
2 changes: 1 addition & 1 deletion modules/nf-core/cellranger/mkfastq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@ process CELLRANGER_MKFASTQ {
tuple val(meta), path(csv), path(bcl)

output:
tuple val(meta), path("*_outs/outs/fastq_path/*.fastq.gz"), emit: fastq
tuple val(meta), path("*_outs/outs/fastq_path/{*.fastq.gz,**/*.fastq.gz}"), emit: fastq
tuple val(meta), path("*_outs/outs/fastq_path/Reports") , emit: reports
tuple val(meta), path("*_outs/outs/fastq_path/Stats") , emit: stats
tuple val(meta), path("*_outs/outs/interop_path/*.bin") , emit: interop
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/cellrangerarc/mkfastq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process CELLRANGERARC_MKFASTQ {

output:
path "versions.yml", emit: versions
path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq
path "${bcl.getSimpleName()}/outs/fastq_path/{*.fastq.gz,**/*.fastq.gz}" , emit: fastq

when:
task.ext.when == null || task.ext.when
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/cellrangeratac/mkfastq/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@ process CELLRANGERATAC_MKFASTQ {

output:
path "versions.yml", emit: versions
path "${bcl.getSimpleName()}/outs/fastq_path/*.fastq.gz" , emit: fastq
path "${bcl.getSimpleName()}/outs/fastq_path/{*.fastq.gz,**/*.fastq.gz}" , emit: fastq

when:
task.ext.when == null || task.ext.when
Expand Down
Loading