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Use apptainer-aware container syntax for gcta/addgrms
1 parent 5962c65 commit 0f36baf

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Lines changed: 3 additions & 5 deletions

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  • modules/nf-core/gcta/addgrms

modules/nf-core/gcta/addgrms/main.nf

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -2,7 +2,7 @@ process GCTA_ADDGRMS {
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tag "${meta.id}"
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label 'process_medium'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/46/46b0d05f0daa47561d87d2a9cac5e51edc2c78e26f1bbab439c688386241a274/data'
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: 'community.wave.seqera.io/library/gcta:1.94.1--9bc35dc424fcf6e9'}"
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@@ -17,17 +17,15 @@ process GCTA_ADDGRMS {
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task.ext.when == null || task.ext.when
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script:
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def extra_args = task.ext.args ?: ''
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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gcta \\
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--mgrm ${mgrm_file} \\
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--make-grm \\
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--out ${prefix} \\
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--thread-num ${task.cpus} \\
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${extra_args}
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${args}
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"""
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stub:

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