Merge branch 'patch_2_5_1' of github.com:maxibor/mag into add_cat_2_s…

…ummary
nf-core · Jan 26, 2024 · fa93107 · fa93107
2 parents 99f9aa8 + 3f3505a
commit fa93107
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Showing 7 changed files with 20 additions and 12 deletions.
diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
@@ -18,11 +18,11 @@
                 "python.linting.flake8Path": "/opt/conda/bin/flake8",
                 "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle",
                 "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle",
-                "python.linting.pylintPath": "/opt/conda/bin/pylint"
+                "python.linting.pylintPath": "/opt/conda/bin/pylint",
             },
 
             // Add the IDs of extensions you want installed when the container is created.
-            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
-        }
-    }
+            "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"],
+        },
+    },
 }
diff --git a/modules.json b/modules.json
@@ -118,7 +118,7 @@
                     },
                     "gtdbtk/classifywf": {
                         "branch": "master",
-                        "git_sha": "898259a38563f29c3c5d2490876019ec2d6f49c5",
+                        "git_sha": "9bbc6a88ce3004ae4bc9f84cef762484dc2c95e5",
                         "installed_by": ["modules"]
                     },
                     "gunc/downloaddb": {

diff --git a/modules/nf-core/gtdbtk/classifywf/environment.yml b/modules/nf-core/gtdbtk/classifywf/environment.yml
diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf
diff --git a/modules/nf-core/gtdbtk/classifywf/meta.yml b/modules/nf-core/gtdbtk/classifywf/meta.yml
diff --git a/subworkflows/local/gtdbtk.nf b/subworkflows/local/gtdbtk.nf
@@ -53,7 +53,7 @@ workflow GTDBTK {
     ch_filtered_bins = bins
         .transpose()
         .map { meta, bin -> [bin.getName(), bin, meta]}
-        .join(ch_bin_metrics, failOnDuplicate: true, failOnMismatch: false)
+        .join(ch_bin_metrics, failOnDuplicate: true)
         .map { bin_name, bin, meta, completeness, contamination -> [meta, bin, completeness, contamination] }
         .branch {
             passed: (it[2] != -1 && it[2] >= params.gtdbtk_min_completeness && it[3] != -1 && it[3] <= params.gtdbtk_max_contamination)
@@ -88,8 +88,6 @@ workflow GTDBTK {
         GTDBTK_CLASSIFYWF.out.summary.map{it[1]}.collect().ifEmpty([]),
         [],
         []
-        // GTDBTK_CLASSIFYWF.out.filtered.map{it[1]}.collect().ifEmpty([]),
-        // GTDBTK_CLASSIFYWF.out.failed.map{it[1]}.collect().ifEmpty([])
     )
 
     emit:

diff --git a/workflows/mag.nf b/workflows/mag.nf
@@ -937,11 +937,13 @@ workflow MAG {
             ch_input_for_postbinning_bins_unbins,
             ch_cat_db
         )
+        // Group all classification results for each sample in a single file
         ch_cat_summary = CAT.out.tax_classification_names
             .collectFile(keepHeader: true) {
                     meta, classification ->
                     ["${meta.id}.txt", classification]
             }
+        // Group all classification results for the whole run in a single file
         CAT_SUMMARY(
             ch_cat_summary.collect()
         )