Remove custom params in GTDBTK/CLASSIFYWF (nf-core#6651)

* Use the proper version calling now implemented * Remove custom params * Fix test
herpov · Oct 2, 2024 · ba1eab2 · ba1eab2
1 parent a924fc4
commit ba1eab2
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Showing 3 changed files with 10 additions and 9 deletions.
diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf
@@ -7,6 +7,7 @@ process GTDBTK_CLASSIFYWF {
     input:
     tuple val(meta)   , path("bins/*")
     tuple val(db_name), path("database/*")
+    val use_pplacer_scratch_dir
     path mash_db
 
     output:
@@ -26,8 +27,8 @@ process GTDBTK_CLASSIFYWF {
 
     script:
     def args = task.ext.args ?: ''
-    def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : ""
-    def mash_mode       = mash_db                       ? "--mash_db ${mash_db}"      : "--skip_ani_screen"
+    def pplacer_scratch = use_pplacer_scratch_dir ? "--scratch_dir pplacer_tmp" : ""
+    def mash_mode       = mash_db                 ? "--mash_db ${mash_db}"      : "--skip_ani_screen"
     prefix = task.ext.prefix ?: "${meta.id}"
 
     """
@@ -43,9 +44,7 @@ process GTDBTK_CLASSIFYWF {
         --out_dir "\${PWD}" \\
         --cpus ${task.cpus} \\
         ${mash_mode} \\
-        ${pplacer_scratch} \\
-        --min_perc_aa ${params.gtdbtk_min_perc_aa} \\
-        --min_af ${params.gtdbtk_min_af}
+        ${pplacer_scratch}
 
     ## If mash db given, classify/ and identify/ directories won't be created
     if [[ -d classify/ && \$(ls -A classify/) ]]; then

diff --git a/modules/nf-core/gtdbtk/classifywf/meta.yml b/modules/nf-core/gtdbtk/classifywf/meta.yml
@@ -30,6 +30,9 @@ input:
       type: file
       description: The local copy of the taxonomic database used by GTDB-tk (unzipped copy)
       pattern: "*"
+  - use_pplacer_scratch_dir:
+      type: boolean
+      description: Set to true to reduce pplacer memory usage by writing to disk (slower)
   - mash_db:
       type: file
       description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional)

diff --git a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test
@@ -26,7 +26,8 @@ nextflow_process {
                         ]
                     ]
                 input[1] = [[], []]
-                input[2] = []
+                input[2] = false
+                input[3] = []
                 """
             }
         }
@@ -35,9 +36,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-           )
+            )
         }
-
     }
-
 }