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Set containerOptions for gatkspark in module #12637

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Merged
FriederikeHanssen merged 7 commits into from
Aug 11, 2026
Merged

Set containerOptions for gatkspark in module #12637

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5f7509d
move containeroptionsinto module
FriederikeHanssen Aug 7, 2026
34343bd
Bind /etc/passwd only for docker and podman
FriederikeHanssen Aug 10, 2026
6e3e2c9
Fix gatk4spark test configs
FriederikeHanssen Aug 10, 2026
93718d5
Reword comment so nf-core lint can parse the input block
FriederikeHanssen Aug 10, 2026
4139bc2
Drop the docker.runOptions overrides from the test configs
FriederikeHanssen Aug 10, 2026
beb9a45
Take the output format as an input instead of ext.suffix
FriederikeHanssen Aug 10, 2026
8f9c14c
Merge branch 'master' into container-options
FriederikeHanssen Aug 10, 2026
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11 changes: 9 additions & 2 deletions modules/nf-core/gatk4spark/applybqsr/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,18 @@ 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" for 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 ['docker', 'podman'] ? '-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
path fai
path dict
val output_suffix

output:
tuple val(meta), path("${prefix}.bam"), emit: bam, optional: true
Expand All @@ -26,7 +33,7 @@ process GATK4SPARK_APPLYBQSR {
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
// suffix can only be bam or cram, cram being the sensible default
def suffix = task.ext.suffix && task.ext.suffix == "bam" ? "bam" : "cram"
def suffix = output_suffix == "bam" ? "bam" : "cram"
def interval_command = intervals ? "--intervals ${intervals}" : ""

def avail_mem = 3072
Expand All @@ -51,7 +58,7 @@ process GATK4SPARK_APPLYBQSR {

stub:
prefix = task.ext.prefix ?: "${meta.id}"
def suffix = task.ext.suffix ?: "cram"
def suffix = output_suffix == "bam" ? "bam" : "cram"
"""
touch ${prefix}.${suffix}
if [[ ${suffix} == bam ]]; then
Expand Down
3 changes: 3 additions & 0 deletions modules/nf-core/gatk4spark/applybqsr/meta.yml
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Expand Up @@ -57,6 +57,9 @@ input:
description: GATK sequence dictionary
pattern: "*.dict"
ontologies: []
- output_suffix:
type: string
description: Output file format, either "bam" or "cram" (cram is the default)
output:
bam:
- - meta:
Expand Down
19 changes: 6 additions & 13 deletions modules/nf-core/gatk4spark/applybqsr/tests/main.nf.test
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Expand Up @@ -2,7 +2,6 @@ nextflow_process {

name "Test Process GATK4SPARK_APPLYBQSR"
script "../main.nf"
config "./nextflow.config"
process "GATK4SPARK_APPLYBQSR"

tag "modules"
Expand All @@ -13,10 +12,6 @@ nextflow_process {
test("sarscov2 - bam") {

when {
params {
module_suffix = "bam"
}

process {
"""
input[0] = [
Expand All @@ -29,6 +24,7 @@ nextflow_process {
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
input[4] = "bam"
"""
}
}
Expand Down Expand Up @@ -56,6 +52,7 @@ nextflow_process {
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
input[4] = "cram"
"""
}
}
Expand All @@ -74,10 +71,6 @@ nextflow_process {
test("sarscov2 - bam - intervals") {

when {
params {
module_suffix = "bam"
}

process {
"""
input[0] = [
Expand All @@ -90,6 +83,7 @@ nextflow_process {
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
input[4] = "bam"
"""
}
}
Expand Down Expand Up @@ -117,6 +111,7 @@ nextflow_process {
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
input[4] = "cram"
"""
}
}
Expand Down Expand Up @@ -149,6 +144,7 @@ nextflow_process {
input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true)
input[4] = "cram"
"""
}
}
Expand All @@ -165,10 +161,6 @@ nextflow_process {

options "-stub"
when {
params {
module_suffix = "bam"
}

process {
"""
input[0] = [
Expand All @@ -181,6 +173,7 @@ nextflow_process {
input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true)
input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true)
input[4] = "bam"
"""
}
}
Expand Down
7 changes: 0 additions & 7 deletions modules/nf-core/gatk4spark/applybqsr/tests/nextflow.config
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6 changes: 6 additions & 0 deletions modules/nf-core/gatk4spark/baserecalibrator/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,12 @@ 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" for 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 ['docker', 'podman'] ? '-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
1 change: 0 additions & 1 deletion modules/nf-core/gatk4spark/baserecalibrator/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ nextflow_process {

name "Test Process GATK4SPARK_BASERECALIBRATOR"
script "../main.nf"
config "./nextflow.config"
process "GATK4SPARK_BASERECALIBRATOR"

tag "modules"
Expand Down
1 change: 0 additions & 1 deletion modules/nf-core/gatk4spark/baserecalibrator/tests/nextflow.config
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6 changes: 6 additions & 0 deletions modules/nf-core/gatk4spark/markduplicates/main.nf
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Expand Up @@ -7,6 +7,12 @@ 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" for 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 ['docker', 'podman'] ? '-v /etc/passwd:/etc/passwd:ro -v /etc/group:/etc/group:ro' : '' }

input:
tuple val(meta), path(bam)
path fasta
Expand Down
1 change: 0 additions & 1 deletion modules/nf-core/gatk4spark/markduplicates/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@ nextflow_process {

name "Test Process GATK4SPARK_MARKDUPLICATES"
script "../main.nf"
config "./nextflow.config"
process "GATK4SPARK_MARKDUPLICATES"

tag "modules"
Expand Down
1 change: 0 additions & 1 deletion modules/nf-core/gatk4spark/markduplicates/tests/nextflow.config
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