Fix linting, fix dastool input bug

sanger-tol · Dec 6, 2024 · 59ede17 · 59ede17
1 parent ebec246
commit 59ede17
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Showing 8 changed files with 123 additions and 25 deletions.
diff --git a/modules.json b/modules.json
@@ -43,7 +43,7 @@
                     },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "97321eded31a12598837a476d3615300af413bb7",
+                        "git_sha": "caab1314ca62679b629da4c79afa9a4cab2bb8ee",
                         "installed_by": ["modules"]
                     },
                     "gtdbtk/classifywf": {

diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf
diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test
diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap
diff --git a/modules/nf-core/gawk/tests/nextflow.config b/modules/nf-core/gawk/tests/nextflow.config
diff --git a/modules/nf-core/gawk/tests/nextflow_with_program_file.config b/modules/nf-core/gawk/tests/nextflow_with_program_file.config
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -105,8 +105,8 @@
                 }
             }
         },
-        "new_group_2": {
-            "title": "New Group 2",
+        "pipeline_options": {
+            "title": "Pipeline options",
             "type": "object",
             "description": "",
             "default": "",
@@ -140,8 +140,8 @@
                 }
             }
         },
-        "new_group_1": {
-            "title": "New Group 1",
+        "bin_taxonomy_options": {
+            "title": "Bin taxonomy options",
             "type": "object",
             "description": "",
             "default": "",
@@ -157,7 +157,10 @@
                 "gtdbtk_db": {
                     "type": "string"
                 },
-                "gtdbtk_mash_db": {
+                "gtdb_bac120_metadata": {
+                    "type": "string"
+                },
+                "gtdb_ar53_metadata": {
                     "type": "string"
                 },
                 "gtdbtk_min_completeness": {
@@ -303,13 +306,13 @@
             "$ref": "#/$defs/bin_refinement_options"
         },
         {
-            "$ref": "#/$defs/new_group_2"
+            "$ref": "#/$defs/pipeline_options"
         },
         {
             "$ref": "#/$defs/bin_qc_options"
         },
         {
-            "$ref": "#/$defs/new_group_1"
+            "$ref": "#/$defs/bin_taxonomy_options"
         },
         {
             "$ref": "#/$defs/institutional_config_options"

diff --git a/workflows/longreadmag.nf b/workflows/longreadmag.nf
@@ -62,7 +62,7 @@ workflow LONGREADMAG {
                 BIN_REFINEMENT(
                     ASSEMBLY.out.assemblies,
                     ASSEMBLY.out.proteins,
-                    BINNING.out.bins
+                    BINNING.out.contig2bin
                 )
             }