Fixed current Zenodo URL of Kmerfinderdb

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database.
 - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues.
 - [#153](https://github.com/nf-core/bacass/pull/153) Update `.nf-core.yml` to fix files_unchanged section for accurate linting checks.
 

conf/test_full.config

@@ -17,6 +17,6 @@ params {
     // Input data for full size test
     input                       = params.pipelines_testdata_base_path + 'bacass/bacass_full.tsv'
     kraken2db                   = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz'
-    kmerfinderdb                = 'https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz'
+    kmerfinderdb                = 'https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz'
     ncbi_assembly_metadata      = 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt'
 }

modules/local/kmerfinder.nf

@@ -8,7 +8,8 @@ process KMERFINDER {
         'biocontainers/kmerfinder:3.0.2--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(reads), path(kmerfinder_db)
+    tuple val(meta), path(reads), path(kmerfinderdb_path)
+    val tax_group
 
     output:
     tuple val(meta), path("*_results.txt")  , emit: report
@@ -18,14 +19,15 @@ process KMERFINDER {
     script:
     def prefix   = task.ext.prefix ?: "${meta.id}"
     def in_reads = reads[0] && reads[1] ? "${reads[0]} ${reads[1]}" : "${reads}"
-    // WARNING: Ensure to update software version in this line if you modify the container/environment.
+    // WARNING: Ensure to update software or database version in this line if you modify the container/environment.
     def kmerfinder_version = "3.0.2"
+    def kmerfinderdb_version = "20190108"
     """
     kmerfinder.py \\
         --infile $in_reads \\
         --output_folder . \\
-        --db_path ${kmerfinder_db}/bacteria.ATG \\
-        -tax ${kmerfinder_db}/bacteria.name \\
+        --db_path ${kmerfinderdb_path}/${tax_group}/bacteria.ATG \\
+        -tax ${kmerfinderdb_path}/${tax_group}/bacteria.name \\
         -x
 
     mv results.txt ${prefix}_results.txt
@@ -34,6 +36,7 @@ process KMERFINDER {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         kmerfinder: \$(echo "${kmerfinder_version}")
+        kmerfinderdb: \$(echo "${kmerfinderdb_version}")
     END_VERSIONS
     """
 }

nextflow_schema.json

@@ -83,7 +83,7 @@
                 },
                 "kmerfinderdb": {
                     "type": "string",
-                    "description": "Path to the Kmerfinder bacteria database. For more details, see [Kmerfinder Databases](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/). You can also download precomputed Kmerfinder database (dated 2019/01/08) from https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz "
+                    "description": "Path to the Kmerfinder bacteria database. For more details, see [Kmerfinder Databases](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/). You can also download precomputed Kmerfinder database (dated 2019/01/08) from https://zenodo.org/records/13447056/files/20190108_kmerfinder_stable_dirs.tar.gz"
                 },
                 "reference_fasta": {
                     "type": "string",
@@ -95,7 +95,7 @@
                 },
                 "ncbi_assembly_metadata": {
                     "type": "string",
-                    "description": "Master file (*.txt) containing a summary of assemblies available in GeneBank or RefSeq. See: https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt"
+                    "description": "Master file (*.txt) containing a summary of assemblies available in GeneBank or RefSeq. See: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt"
                 }
             }
         },

subworkflows/local/kmerfinder_subworkflow.nf

@@ -33,7 +33,8 @@ workflow KMERFINDER_SUBWORKFLOW {
         .set{ ch_to_kmerfinder }
 
     KMERFINDER (
-        ch_to_kmerfinder
+        ch_to_kmerfinder,    // Channel: [ meta, reads, path_to_kmerfinderdb ]
+        'bacteria'           // Val: 'tax_group'
     )
     ch_kmerfinder_report    = KMERFINDER.out.report
     ch_kmerfinder_json      = KMERFINDER.out.json