miga-base 1.3.20.2 → 1.3.20.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0ed682917cf2e5645f7ae31789932c2d14eaf06faa29aca1b13142862f653d49
-  data.tar.gz: fce8e42084a3896c49a01ce603d0c99ac766b1bade878b43ac55fd5be11ba523
+  metadata.gz: c6cd171c44ec3139121607db27badddcd12e8cefd45f49acc6bc5f018184943f
+  data.tar.gz: 8ca59c51be7224fb7e0d3b0561cb72ef9f95594a2b51fa9a3c04c65ab60d7b66
 SHA512:
-  metadata.gz: 1eacee695bac46bbed8c1bb13694c2ff614020eef89d8547939a6d976f21659464185d648ff2244f25e5ddba2ae429a1d87758034eefa48ce84e8636f072c686
-  data.tar.gz: 04fb36c2c58b9fde72e48f9a9983a3505f6368ac231e412c7844380fa4a497dcd71d3209c09b97d961f393b6b3c9965092e72620b88d226fa4275a3a8993db0d
+  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, 2].freeze
+  VERSION = [1.3, 20, 3].freeze
 
   ##
   # Nickname for the current major.minor version.

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
@@ -27,8 +35,6 @@ case "$TYPE" in
     P_LEN=0
     BEST_CT=0
     PROCEDURE=single
-    ASM_LEN=$(grep -v '^>' "../05.assembly/${DATASET}.LargeContigs.fna" \
-      | wc -lc | awk '{ print $2-$1 }')
     [[ "$ASM_LEN" -lt 2000 ]] && PROCEDURE=meta
     echo "# Codon table selection:" > "${DATASET}.ct.t"
     for ct in 11 4 ; do

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.20.2
+  version: 1.3.20.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R