miga-base 1.3.15.0 → 1.3.15.2

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: c98ad5733d0f008f1aa18156c20f0fe59c7b30f1c2a7fadb213840c46bdd91fc
-  data.tar.gz: 794e59380b68c9dc2f62e3f5241e7fb0aa7436f7837693dea90da56c4d4b371c
+  metadata.gz: f897211099d0c1b049576951a3810ed33185d5b4519d72a5b7490b8b41bc0b6f
+  data.tar.gz: 6858281155d41c5954c144cda09156994640cf6ea3b34764456961dfa8554f4a
 SHA512:
-  metadata.gz: e44d171e1ab9313d67f2fd3782335c3467ec9b61f425483539fd1c9691c572ecaee229a10529faac5cfd9314b350d54d427dd94c19496d1d71c81a554e7c6687
-  data.tar.gz: 8b7f5b9ad54e08c3ad0ebdc2a6b24022a275259bddc6c579a1313f113d54a31a35f4fc761059491ec79e50d29fc3dd85687c53cd63479c8a1938f492a4bac9fa
+  metadata.gz: 292bdf4161b612675fd39e454d64c00bba54b0ac6e9b02471e32e2dfebd19321a6008304490b78c3b3926a25bd2f4a7d92bf7f407541c0069d9171caec7efc1b
+  data.tar.gz: e2705c2f55c776b4f117f2549d1b6d7d212be7c73b9efb08030ee9732179a09347df431512ad2fa794661d2e2a1005e4908bf273b18b95802afe4a2828484a2b

data/lib/miga/dataset/result/add.rb

@@ -261,10 +261,12 @@ module MiGA::Dataset::Result::Add
   def add_result_distances_nonref(base)
     return nil unless
       result_files_exist?(base, %w[.aai-medoids.tsv .aai.db]) ||
-      result_files_exist?(base, %w[.ani-medoids.tsv .ani.db])
+      result_files_exist?(base, %w[.ani-medoids.tsv .ani.db]) ||
+      result_files_exist?(base, %w[.empty])
 
     add_files_to_ds_result(
       MiGA::Result.new("#{base}.json"), name,
+      empty: '.empty',
       aai_medoids: '.aai-medoids.tsv',
       haai_db: '.haai.db',
       aai_db: '.aai.db',

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, 15, 0].freeze
+  VERSION = [1.3, 15, 2].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, 5, 2)
+  VERSION_DATE = Date.new(2024, 5, 21)
 
   ##
   # References of MiGA

data/scripts/cds.bash

@@ -64,7 +64,7 @@ fi
 
 # Gzip
 for ext in gff3 faa fna ; do
-  [[ -e "$DATASET.$ext" ]] && gzip -9 -f "$DATASET.$ext"
+  [[ -e "$DATASET.$ext" ]] && gzip -9f "$DATASET.$ext"
 done
 
 # Finalize

data/scripts/distances.bash

@@ -29,44 +29,46 @@ blast=no
 blat=no
 diamond=no
 fastani=no
-case $(miga option -P "$PROJECT" -k haai_p) in
-  fastaai)
-    fastaai=yes
-    ;;
-  diamond)
-    diamond=yes
-    aai=yes
-    ;;
-  blast)
-    blast=yes
-    aai=yes
-    ;;
-esac
+if [[ ! -s "${DATASET}.empty" ]] ; then
+  case $(miga option -P "$PROJECT" -k haai_p) in
+    fastaai)
+      fastaai=yes
+      ;;
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
 
-case $(miga option -P "$PROJECT" -k aai_p) in
-  diamond)
-    diamond=yes
-    aai=yes
-    ;;
-  blast)
-    blast=yes
-    aai=yes
-    ;;
-esac
+  case $(miga option -P "$PROJECT" -k aai_p) in
+    diamond)
+      diamond=yes
+      aai=yes
+      ;;
+    blast)
+      blast=yes
+      aai=yes
+      ;;
+  esac
 
-case $(miga option -P "$PROJECT" -k ani_p) in
-  blast)
-    blast=yes
-    ani=yes
-    ;;
-  blat)
-    blat=yes
-    ani=yes
-    ;;
-  fastani)
-    fastani=yes
-    ;;
-esac
+  case $(miga option -P "$PROJECT" -k ani_p) in
+    blast)
+      blast=yes
+      ani=yes
+      ;;
+    blat)
+      blat=yes
+      ani=yes
+      ;;
+    fastani)
+      fastani=yes
+      ;;
+  esac
+fi
 
 
 miga date > "${DATASET}.done"

data/scripts/miga.bash

@@ -15,6 +15,11 @@ function exists { [[ -e "$1" ]] ; }
 # Evaluates if the first passed argument is a function
 function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
 
+# Override gzip with pigz (if available)
+if which -s pigz ; then
+  function gzip { pigz -p ${CORES:-2} "$@" ; }
+fi
+
 # Initiate a project-wide run
 function miga_start_project_step {
   local dir="$1"

data/scripts/mytaxa.bash

@@ -86,12 +86,10 @@ else
     ktImportText -o "$DATASET.html" -n biota "$DATASET.mytaxa.krona,$DATASET"
 
     # Gzip and cleanup
-    [[ -e "../../../06.cds/$DATASET.gff2" ]] \
-      && gzip -9 -f "../../../06.cds/$DATASET.gff2"
-    [[ -e "../../../06.cds/$DATASET.gff3" ]] \
-      && gzip -9 -f "../../../06.cds/$DATASET.gff3"
-    gzip -9 -f "$DATASET.mytaxain"
-    gzip -9 -f "$DATASET.blast"
+    for i in "../../../06.cds/$DATASET.gff2" "../../../06.cds/$DATASET.gff3" \
+             "$DATASET.mytaxain" "$DATASET.blast" ; do
+      [[ -e $i ]] && gzip -9f $i
+    done
     rm "$DATASET.daa"
   fi
 

data/scripts/mytaxa_scan.bash

@@ -72,7 +72,7 @@ else
         awk "NR==$win" "$DATASET.wintax.genes" | tr "\\t" "\\n" \
           > "$DATASET.reg/$i.ids"
         if [[ "$FAA" == *.gz ]] ; then
-          gzip -c -d "$FAA" \
+          gzip -cd "$FAA" \
             | FastA.filter.pl -q "$DATASET.reg/$i.ids" /dev/stdin \
             > "$DATASET.reg/$i.faa"
         else
@@ -81,8 +81,7 @@ else
         fi
       done
       # Archive regions
-      tar -cf "$DATASET.reg.tar" "$DATASET.reg"
-      gzip -9 "$DATASET.reg.tar"
+      tar -c "$DATASET.reg" | gzip -9c > "$DATASET.reg.tar.gz"
       rm -r "$DATASET.reg"
     fi
 
@@ -91,7 +90,7 @@ else
       [[ -e "$DATASET.$x" ]] && rm "$DATASET.$x"
     done
     [[ -s "$DATASET.mytaxa" && ! -s "$DATASET.mytaxa.gz" ]] \
-      && gzip -9 -f "$DATASET.mytaxa"
+      && gzip -9f "$DATASET.mytaxa"
   fi
 
 fi

data/scripts/ssu.bash

@@ -59,7 +59,7 @@ if [[ -s $fa ]] ; then
 
   # Gzip
   for x in gff ssu.all.fa rdp.tsv trna.txt ; do
-    [[ -e "${DATASET}.${x}" ]] && gzip -9 -f "${DATASET}.${x}"
+    [[ -e "${DATASET}.${x}" ]] && gzip -9f "${DATASET}.${x}"
   done
 fi
 

data/scripts/trimmed_reads.bash

@@ -30,7 +30,8 @@ FastQ.tag.rb -i "$in1" -p "$b-" -s "/1" -o "$b.1.fastq.gz"
 [[ -e "$in2" ]] && FastQ.tag.rb -i "$in2" -p "$b-" -s "/2" -o "$b.2.fastq.gz"
 
 # Multitrim
-CMD="multitrim.py --zip gzip --level 9 --threads $CORES -o $b"
+CMD="multitrim.py --level 9 --threads $CORES -o $b"
+which -s pigz && CMD="$CMD --zip pigz"
 if [[ -s "$b.2.fastq.gz" ]] ; then
   # Paired
   $CMD -1 "$b.1.fastq.gz" -2 "$b.2.fastq.gz"

data/utils/distance/runner.rb

@@ -35,7 +35,7 @@ class MiGA::DistanceRunner
 
   # Launch the appropriate analysis
   def go!
-    $stderr.puts "Launching analysis"
+    $stderr.puts 'Launching analysis'
     return if dataset.multi?
 
     Dir.mktmpdir do |tmp_dir|
@@ -68,6 +68,14 @@ class MiGA::DistanceRunner
   # Launch analysis for query datasets
   def go_query!
     $stderr.puts 'Launching analysis for query dataset'
+
+    # Check if the project is empty
+    if ref_project.dataset_ref_active.empty?
+      out_base = File.expand_path(dataset.name, home)
+      File.open("#{out_base}.empty", 'w') { |fh| fh.puts 'Empty ref_project' }
+      return
+    end
+
     # Check if project is ready
     tsk = ref_project.clade? ? [:subclades, :ani] : [:clade_finding, :aai]
     res = ref_project.result(tsk[0])

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.15.0
+  version: 1.3.15.2
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-05-02 00:00:00.000000000 Z
+date: 2024-05-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons