Fix linting, update dastool + metabat2 modules, fix renamed modules

sanger-tol · Dec 12, 2024 · b6f807a · b6f807a
1 parent 05c8326
commit b6f807a
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Showing 23 changed files with 1,197 additions and 96 deletions.
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -38,8 +38,6 @@ lint:
     - validation.summary.afterText
   readme:
     - nextflow_badge
-    - nextflow_badge
-    - nextflow_badge
 nf_core_version: 3.0.2
 org_path: null
 repository_type: pipeline

diff --git a/bin/extract_ncbi_name.awk b/bin/extract_ncbi_name.awk
@@ -1,18 +1,24 @@
-BEGIN { 
+## Extact the highest level NCBI rank converted by the
+## gtdb_to_ncbi_majority_vote.py script and save it to
+## a new column to parse with taxonkit.
+##
+## Author: Jim Downie, December 2024
+
+BEGIN {
     FS = "\t"
     OFS = FS
 }
-NR == 1 { print $1, $2, $3, "name" }
+NR == 1 { print $1, $2, $3, "name", "taxid" }
 NR > 1 {
-	if($0 ~ /Unclassified/) {
-		print $1, $2, $3, $3
-		next
-	}
+    if($0 ~ /Unclassified/) {
+        print $1, $2, $3, $3
+        next
+    }
     n_elem = split($3, names, /;?[[:alpha:]]__/)
     for(i = n_elem; i > 1; i--) {
-		if(names[i] != "") {
+        if(names[i] != "") {
             print $1, $2, $3, names[i]
-			break
+            break
         }
     }
-}
+}
diff --git a/modules.json b/modules.json
@@ -33,12 +33,12 @@
                     },
                     "dastool/dastool": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6d736588f4af4bc9b615bd7189442bd4272ae26e",
                         "installed_by": ["modules"]
                     },
                     "dastool/fastatocontig2bin": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6d736588f4af4bc9b615bd7189442bd4272ae26e",
                         "installed_by": ["modules"]
                     },
                     "gawk": {
@@ -66,7 +66,7 @@
                     },
                     "metabat2/metabat2": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "6d736588f4af4bc9b615bd7189442bd4272ae26e",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/metabat2/metabat2/metabat2-metabat2.diff"
                     },

diff --git a/modules/nf-core/dastool/dastool/environment.yml b/modules/nf-core/dastool/dastool/environment.yml
diff --git a/modules/nf-core/dastool/dastool/main.nf b/modules/nf-core/dastool/dastool/main.nf
diff --git a/modules/nf-core/dastool/dastool/meta.yml b/modules/nf-core/dastool/dastool/meta.yml
diff --git a/modules/nf-core/dastool/dastool/tests/main.nf.test b/modules/nf-core/dastool/dastool/tests/main.nf.test