Merge pull request #183 from nf-core/update-bracken-params

Update bracken so parameters come directly from database args

modules.json

@@ -23,7 +23,7 @@
                     },
                     "bracken/bracken": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "8cab56516076b23c6f8eb1ac20ba4ce9692c85e1"
                     },
                     "cat/fastq": {
                         "branch": "master",

modules/nf-core/bracken/bracken/main.nf

@@ -21,12 +21,9 @@ process BRACKEN_BRACKEN {
     task.ext.when == null || task.ext.when
 
     script:
-    def threshold = meta.threshold ?: 10
-    def taxonomic_level = meta.taxonomic_level ?: 'S'
-    def read_length = meta.read_length ?: 150
-    def args = task.ext.args ?: "-l ${taxonomic_level} -t ${threshold} -r ${read_length}"
+    def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
-    bracken_report = "${prefix}_${taxonomic_level}.tsv"
+    bracken_report = "${prefix}.tsv"
     // WARN: Version information not provided by tool on CLI.
     // Please update version string below when bumping container versions.
     def VERSION = '2.7'

modules/nf-core/bracken/bracken/meta.yml

@@ -1,7 +1,10 @@
 name: bracken_bracken
 description: Re-estimate taxonomic abundance of metagenomic samples analyzed by kraken.
 keywords:
-  - sort
+  - bracken
+  - metagenomics
+  - abundance
+  - kraken2
 tools:
   - bracken:
       description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.