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Update checkM version and add support for pre-defined database (#2125)

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Bump checkM version and add support for pre-defined database

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
This commit is contained in:
James A. Fellows Yates 2022-09-28 14:48:18 +02:00 committed by GitHub
parent 3d7ce93630
commit 0ab15c5ee9
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3 changed files with 14 additions and 7 deletions
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10
modules/checkm/lineagewf/main.nf
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@ -2,14 +2,15 @@ process CHECKM_LINEAGEWF {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
conda (params.enable_conda ? "bioconda::checkm-genome=1.1.3" : null) conda (params.enable_conda ? "bioconda::checkm-genome=1.2.1" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1' : 'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' :
'quay.io/biocontainers/checkm-genome:1.1.3--py_1' }" 'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
val fasta_ext val fasta_ext
path db
output: output:
tuple val(meta), path("${prefix}") , emit: checkm_output tuple val(meta), path("${prefix}") , emit: checkm_output
@ -22,7 +23,10 @@ process CHECKM_LINEAGEWF {
script: script:
def args = task.ext.args ?: '' def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}" prefix = task.ext.prefix ?: "${meta.id}"
checkm_db = db ? "export CHECKM_DATA_PATH=${db}" : ""
""" """
$checkm_db
checkm \\ checkm \\
lineage_wf \\ lineage_wf \\
-t $task.cpus \\ -t $task.cpus \\

3
modules/checkm/lineagewf/meta.yml
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@ -34,6 +34,9 @@ input:
- fasta_ext: - fasta_ext:
type: value type: value
description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas) description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas)
- db:
type: directory
description: Optional directory pointing to checkM database to prevent re-downloading
output: output:
- meta: - meta:

4
tests/modules/checkm/lineagewf/main.nf
View file

@ -10,7 +10,7 @@ workflow test_checkm_lineagewf {
file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['contigs_fasta'], checkIfExists: true) ]
fasta_ext = 'fasta' fasta_ext = 'fasta'
CHECKM_LINEAGEWF ( input, fasta_ext ) CHECKM_LINEAGEWF ( input, fasta_ext, [] )
} }
workflow test_checkm_lineagewf_multi { workflow test_checkm_lineagewf_multi {
@ -20,5 +20,5 @@ workflow test_checkm_lineagewf_multi {
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ] file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] ]
fasta_ext = 'fasta' fasta_ext = 'fasta'
CHECKM_LINEAGEWF ( input, fasta_ext ) CHECKM_LINEAGEWF ( input, fasta_ext, [] )
} }