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

Bump checkM version and add support for pre-defined database

Co-authored-by: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>

modules/checkm/lineagewf/main.nf

@@ -2,14 +2,15 @@ process CHECKM_LINEAGEWF {
     tag "$meta.id"
     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 ?
-        'https://depot.galaxyproject.org/singularity/checkm-genome:1.1.3--py_1' :
-        'quay.io/biocontainers/checkm-genome:1.1.3--py_1' }"
+        'https://depot.galaxyproject.org/singularity/checkm-genome:1.2.1--pyhdfd78af_0' :
+        'quay.io/biocontainers/checkm-genome:1.2.1--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(fasta)
     val fasta_ext
+    path db
 
     output:
     tuple val(meta), path("${prefix}")    , emit: checkm_output
@@ -20,9 +21,12 @@ process CHECKM_LINEAGEWF {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args   ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
+    def args  = task.ext.args   ?: ''
+    prefix    = task.ext.prefix ?: "${meta.id}"
+    checkm_db = db ? "export CHECKM_DATA_PATH=${db}" : ""
     """
+    $checkm_db
+
     checkm \\
         lineage_wf \\
         -t $task.cpus \\

modules/checkm/lineagewf/meta.yml

@@ -34,6 +34,9 @@ input:
   - fasta_ext:
       type: value
       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:
   - meta:

tests/modules/checkm/lineagewf/main.nf

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