tRNAscan conditional on dataset type (genomes)

lib/miga/version.rb

@@ -12,15 +12,15 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 16, 0].freeze
+  VERSION = [1.3, 17, 0].freeze
 
   ##
   # Nickname for the current major.minor version.
   VERSION_NAME = 'mezzotint'
 
   ##
   # Date of the current gem relese.
-  VERSION_DATE = Date.new(2024, 6, 23)
+  VERSION_DATE = Date.new(2024, 6, 28)
 
   ##
   # References of MiGA

manual/part5/workflow.md

@@ -403,7 +403,8 @@ Supported file keys:
 * `gff` (*gz*): GFF v3 file containing the location of detected SSU genes
 * `all_ssu_genes` (*gz*): FastA file containing all the detected SSU genes
 * `classification`: Taxonomic classification with RDP taxonomy
-* `trna_list` (*gz*): Raw-text table with tRNA predictions
+* `trna_list` (*gz*): Raw-text table with tRNA predictions, generated for all
+  genome types (non-multi)
 
 Deprecated file keys (for backwards-compatibility):
 

scripts/ssu.bash

@@ -46,16 +46,17 @@ if [[ -s $fa ]] ; then
       >> "${DATASET}.rdp.tsv"
   fi
 
-  # tRNAscan-SE
-  dom_opt="-$(echo "$d" | perl -pe 's/(\S).*/$1/')"
-  out="${DATASET}.trna.txt"
-  # `echo O` is to avoid a hang from a pre-existing output file.
-  # This is better than pre-checking (and removing), because it avoids
-  # the (unlikely) scenario of a file racing (e.g., a file created right
-  # before tRNAscan-SE starts, or a `rm` failure).
-  #
-  # The trailing `|| true` is to treat failure as non-fatal
-  echo O | tRNAscan-SE $dom_opt -o "${DATASET}.trna.txt" -q "$fa" || true
+  # tRNAscan-SE (only if non-multi)
+  if miga ls -P "$PROJECT" -D "$DATASET" --no-multi --silent ; then
+    dom_opt="-$(echo "$d" | perl -pe 's/(\S).*/$1/')"
+    # `echo O` is to avoid a hang from a pre-existing output file.
+    # This is better than pre-checking (and removing), because it avoids
+    # the (unlikely) scenario of a file racing (e.g., a file created right
+    # before tRNAscan-SE starts, or a `rm` failure).
+    #
+    # The trailing `|| true` is to treat failure as non-fatal
+    echo O | tRNAscan-SE $dom_opt -o "${DATASET}.trna.txt" -q "$fa" || true
+  fi
 
   # Gzip
   for x in gff ssu.all.fa rdp.tsv trna.txt ; do