Skip to content

Set containerOptions for gatkspark in module #12637

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
FriederikeHanssen wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Set containerOptions for gatkspark in module #12637

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
8 changes: 8 additions & 0 deletions modules/nf-core/gatk4spark/applybqsr/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,14 @@ process GATK4SPARK_APPLYBQSR {
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/49/498aea9c9bcaf736b9fb2a01366c1b7b38ccc0d38143178afc325d6a93241447/data'
: 'community.wave.seqera.io/library/gatk4-spark:4.6.2.0--8b5cd67ee60a714e'}"

// Spark's native UnixLoginModule fails to resolve a username for the container's UID
// (LoginException: invalid null input: name), because the container's own /etc/passwd
// has no entry for the host UID that docker.runOptions maps it to. Bind-mounting the
// host's /etc/passwd/group (which do have that entry) fixes the native lookup.
containerOptions { workflow.containerEngine in ['singularity', 'apptainer']
? '--bind /etc/passwd:/etc/passwd:ro,/etc/group:/etc/group:ro'

@pontus pontus Aug 7, 2026

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

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

This shouldn't be needed for singularity/apptainer, it will make sure to provide sensible details.

: '-v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro' }

input:
tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals)
path fasta
Expand Down
8 changes: 8 additions & 0 deletions modules/nf-core/gatk4spark/baserecalibrator/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,14 @@ process GATK4SPARK_BASERECALIBRATOR {
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/49/498aea9c9bcaf736b9fb2a01366c1b7b38ccc0d38143178afc325d6a93241447/data'
: 'community.wave.seqera.io/library/gatk4-spark:4.6.2.0--8b5cd67ee60a714e'}"

// Spark's native UnixLoginModule fails to resolve a username for the container's UID
// (LoginException: invalid null input: name), because the container's own /etc/passwd
// has no entry for the host UID that docker.runOptions maps it to. Bind-mounting the
// host's /etc/passwd/group (which do have that entry) fixes the native lookup.
containerOptions { workflow.containerEngine in ['singularity', 'apptainer']
? '--bind /etc/passwd:/etc/passwd:ro,/etc/group:/etc/group:ro'
: '-v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro' }

input:
tuple val(meta), path(input), path(input_index), path(intervals)
path fasta
Expand Down
8 changes: 8 additions & 0 deletions modules/nf-core/gatk4spark/markduplicates/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,14 @@ process GATK4SPARK_MARKDUPLICATES {
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/49/498aea9c9bcaf736b9fb2a01366c1b7b38ccc0d38143178afc325d6a93241447/data'
: 'community.wave.seqera.io/library/gatk4-spark:4.6.2.0--8b5cd67ee60a714e'}"

// Spark's native UnixLoginModule fails to resolve a username for the container's UID
// (LoginException: invalid null input: name), because the container's own /etc/passwd
// has no entry for the host UID that docker.runOptions maps it to. Bind-mounting the
// host's /etc/passwd/group (which do have that entry) fixes the native lookup.
containerOptions { workflow.containerEngine in ['singularity', 'apptainer']
? '--bind /etc/passwd:/etc/passwd:ro,/etc/group:/etc/group:ro'
: '-v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro' }

input:
tuple val(meta), path(bam)
path fasta
Expand Down
Loading