added correct rm from issue #183 and added score instead of p-value t…

…o deepvirfinder and virfinder
replikation · Mar 3, 2023 · 165bd3d · 165bd3d
1 parent 79faf1a
commit 165bd3d
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diff --git a/submodule_report/Heatmap_table.Rmd b/submodule_report/Heatmap_table.Rmd
@@ -66,7 +66,7 @@ The tool's output and what WtP assigns are shown in the table below.
 
 Tool            | Standard output                     | WtP displayed value | F1 scores by Ho et al.
 |-|-|-|-|
-|deepvirfinder  | p-value: 0 to 1                      | 0 to 1      | >0.83
+|deepvirfinder  | score: 0 to 1                        | 0 to 1      | >0.83
 |metaphinder    | string: phage                        | 1           | >0.83
 |metaphinder own| string: phage                        | 1           | N/A
 |phigaro        | score: 0 to 1                        | 0 to 1      | N/A
@@ -75,7 +75,7 @@ Tool            | Standard output                     | WtP displayed value | F1
 |sourmash       | similarity: 0 to 1                   | 0 to 1      | N/A
 |vibrant        | prediction: virus                    | 1           | >0.83
 |vibrant-virome | prediction: virus                    | 1           | N/A
-|virfinder      | p-value: 0 to 1                      | 0 to 1      | >0.83
+|virfinder      | score: 0 to 1                        | 0 to 1      | >0.83
 |virnet         | score: 0 to 1                        | 0 to 1      | N/A
 |virsorter      | category 1, category 2, category 3   | 1, 0.5, 0   | >0.83
 |virsorter-virome|category 1, category 2, category 3   | 1, 0.5, 0   | N/A

diff --git a/workflows/process/sourmash/download_references.nf b/workflows/process/sourmash/download_references.nf
@@ -18,8 +18,7 @@ process download_references {
         wget --no-check-certificate https://osf.io/6ukfx/download -O references.tar.gz
         tar -xvzf references.tar.gz
         mv references/*.fa .
-        rm -r references
-        references.tar.gz
+        rm -r references.tar.gz
         """
     stub:
         """