miga-base 1.3.15.1 → 1.3.15.3

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA256:
-  metadata.gz: 0b28d0e279592c817bf22a7ada5e292cfae35fff6d64b170499a9b8a9e662e89
-  data.tar.gz: 5653a537b9468d7d4ec9a7a02712be6c3a4481d020909b757cc443ddab50f097
+  metadata.gz: fc7061e7db5ea3abbd360cbb333a80200c7c4ee3ab9f12f9c13e3c780c5d6137
+  data.tar.gz: 3e72007cc93f82eab23bc4663dc0fdf4f609ee1ab5dee2661c7d076e56da07bf
 SHA512:
-  metadata.gz: 9f28050603a5e0a015b284cb09e88621a2650ef0eb6580b9ca6edf362dfd2ae19a50848e476ad9a7f66d4aa8c3a28ed51cdfef1f0566de72d3ba3b6f16596ce6
-  data.tar.gz: 9e0aa59955542a9ac42f009965cc6e66e9fb7d55269298e554652b20afaca312454d1fbff09a08cd2660e9f2cbf33e10f120117ed5f5ddf853d871a4817f2de0
+  metadata.gz: 126fe24613362de8ea56e457294d87846ed6155402f853c12eee7a64ba55a0108fa79f4de52b3fe9a46cf3ede18893ad170fb63189637c12a3074dde107488cf
+  data.tar.gz: 411aeb6de107190ac6d7b1024cf4fd77996ad7f9be2127dec54a12dd6fac9f1659e606e901a2b7a5cc1a0f62363426b23c817beeef3ae77a92f1643532e7b44d

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, 1].freeze
+  VERSION = [1.3, 15, 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, 5, 6)
+  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/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 command -v pigz &>/dev/null ; 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 $b"
+command -v pigz &>/dev/null && CMD="$CMD --zip pigz"
 if [[ -s "$b.2.fastq.gz" ]] ; then
   # Paired
   $CMD -1 "$b.1.fastq.gz" -2 "$b.2.fastq.gz"

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: miga-base
 version: !ruby/object:Gem::Version
-  version: 1.3.15.1
+  version: 1.3.15.3
 platform: ruby
 authors:
 - Luis M. Rodriguez-R
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-05-06 00:00:00.000000000 Z
+date: 2024-05-21 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: daemons