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Add antismash download DB: missing container folders as output channels (#1567)
* Add missing container folders as output channels * Apply suggestions from code review Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update tool name * Update test output checksum Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Jasmin F
GitHub
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3 changed files with 29 additions and 7 deletions
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@ -7,8 +7,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
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'quay.io/biocontainers/antismash-lite:6.0.1--pyhdfd78af_1' }"
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/*
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These files are normally downloaded by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
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These files are normally downloaded/created by download-antismash-databases itself, and must be retrieved for input by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. This is solely for use for CI tests of the nf-core/module version of antiSMASH.
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Reason: Upon execution, the tool checks if certain database files are present within the container and if not, it tries to create them in /usr/local/bin, for which only root user has write permissions. Mounting those database files with this module prevents the tool from trying to create them.
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These files are also emitted as output channels in this module to enable the antismash-lite module to use them as mount volumes to the docker/singularity containers.
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*/
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containerOptions {
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@ -26,6 +27,9 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
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output:
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path("antismash_db") , emit: database
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path("css"), emit: css_dir
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path("detection"), emit: detection_dir
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path("modules"), emit: modules_dir
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path "versions.yml", emit: versions
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when:
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@ -40,7 +44,7 @@ process ANTISMASH_ANTISMASHLITEDOWNLOADDATABASES {
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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antismash: \$(antismash --version | sed 's/antiSMASH //')
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antismash-lite: \$(antismash --version | sed 's/antiSMASH //')
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END_VERSIONS
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"""
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}
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@ -27,17 +27,17 @@ input:
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- database_css:
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type: directory
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description: |
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antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "css"
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- database_detection:
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type: directory
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description: |
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antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "detection"
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- database_modules:
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type: directory
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description: |
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antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the use by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "modules"
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output:
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@ -50,6 +50,21 @@ output:
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type: directory
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description: Download directory for antiSMASH databases
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pattern: "antismash_db"
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- css_dir:
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type: directory
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description: |
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antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "css"
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- detection_dir:
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type: directory
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description: |
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antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "detection"
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- modules_dir:
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type: directory
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description: |
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antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines.
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pattern: "modules"
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authors:
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- "@jasmezz"
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@ -1,14 +1,17 @@
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- name: antismash antismashlitedownloaddatabases test_antismash_antismashlitedownloaddatabases
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command: nextflow run tests/modules/antismash/antismashlitedownloaddatabases -entry test_antismash_antismashlitedownloaddatabases -c tests/config/nextflow.config
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tags:
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- antismash/antismashlitedownloaddatabases
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- antismash
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- antismash/antismashlitedownloaddatabases
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files:
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- path: output/antismash/versions.yml
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md5sum: e2656c8d2bcc7469eba40eb1ee5c91b3
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md5sum: 24859c67023abab99de295d3675a24b6
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- path: output/antismash/antismash_db
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- path: output/antismash/antismash_db/clusterblast
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- path: output/antismash/antismash_db/clustercompare
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- path: output/antismash/antismash_db/pfam
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- path: output/antismash/antismash_db/resfam
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- path: output/antismash/antismash_db/tigrfam
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- path: output/antismash/css
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- path: output/antismash/detection
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- path: output/antismash/modules
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