miga-base 1.3.20.1 → 1.3.20.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c6c4afd4c7ece4cbb7c188d59b1743b149e1b721a44f12dfa90e47d960716266
-  data.tar.gz: cb37cb26f5ced17d58172ca00f90860a984071c628878f4e65ecf019347cda7d
+  metadata.gz: c6cd171c44ec3139121607db27badddcd12e8cefd45f49acc6bc5f018184943f
+  data.tar.gz: 8ca59c51be7224fb7e0d3b0561cb72ef9f95594a2b51fa9a3c04c65ab60d7b66
 SHA512:
-  metadata.gz: de3a104391e4742b5fa26ed4e96c35ca64780d244c591895a9465089825e11d5521d301467daf520fb06acbe837afc0fc0f75da26fdbc19fdff78cfb31085d53
-  data.tar.gz: 746203077d5ec8a48b85129324b954cfa587a89a3f9eee4c0dc23075925ad3ecf2649b251979ac0e03ef8fc4f18f68f03afc4a72df034f18b134d3ffda1f0075
+  metadata.gz: 281aa0434dbeb5d4d5c69e5df44a459e77d22ce1664c68553fe61c04640ec27128002428aaffca3f1913973d2cb689afba51e683f7e3ca594bfede38b1ad79be
+  data.tar.gz: 2f37a8bc9fd5e516a669185b56e71339fca60314d7505917e1c4d4291801c81f4d9a3a36988e63bf0e0829d63046b3dc1b34c072a893449df2b63aa849cb1a05

data/lib/miga/version.rb

@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 20, 1].freeze
+  VERSION = [1.3, 20, 3].freeze
 
   ##
   # Nickname for the current major.minor version.
@@ -20,7 +20,7 @@ module MiGA
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 7, 25)
+  VERSION_DATE = Date.new(2024, 8, 29)
 
   ##
   # References of MiGA

data/scripts/cds.bash

@@ -16,6 +16,14 @@ if [[ -e "../05.assembly/$DATASET.LargeContigs.fna.gz" \
   miga add_result -P "$PROJECT" -D "$DATASET" -r assembly -f
 fi
 
+# Check if the input assembly is empty
+ASM_LEN=$(grep -v '^>' "../05.assembly/${DATASET}.LargeContigs.fna" \
+            | wc -lc | awk '{ print $2-$1 }')
+if [[ "$ASM_LEN" -lt 1 ]] ; then
+  miga edit -P "$PROJECT" -D "$DATASET" --inactivate "Empty assembly"
+  exit 0
+fi
+
 # Run Prodigal
 TYPE=$(miga ls -P "$PROJECT" -D "$DATASET" -m type | cut -f 2)
 case "$TYPE" in
@@ -26,10 +34,12 @@ case "$TYPE" in
   *)
     P_LEN=0
     BEST_CT=0
+    PROCEDURE=single
+    [[ "$ASM_LEN" -lt 2000 ]] && PROCEDURE=meta
     echo "# Codon table selection:" > "${DATASET}.ct.t"
     for ct in 11 4 ; do
       prodigal -a "${DATASET}.faa.$ct" -d "${DATASET}.fna.$ct" \
-        -o "${DATASET}.gff3.$ct" -f gff -q -p single -g "$ct" \
+        -o "${DATASET}.gff3.$ct" -f gff -q -p $PROCEDURE -g "$ct" \
         -i "../05.assembly/${DATASET}.LargeContigs.fna"
       C_LEN=$(grep -v '^>' "${DATASET}.faa.$ct" \
         | perl -pe 's/[^A-Z]//ig' | wc -c | awk '{print $1}')

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.20.1
+  version: 1.3.20.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-07-25 00:00:00.000000000 Z
+date: 2024-08-29 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons