Collect the most accurate alignment statistic. (#9210)

See nf-core/pairgenomealign#96

Author: charles-plessy

modules/nf-core/last/train/main.nf

@@ -34,7 +34,9 @@ process LAST_TRAIN {
 
     echo "id\tsubstitution_percent_identity\tlast -t\tlast -a\tlast -A\tlast -b\tlast -B\tlast -S"         > ${prefix}.train.tsv
     printf "\$(basename ${prefix}.train .target.train)\t"                                                 >> ${prefix}.train.tsv
-    grep 'substitution percent identity' ${prefix}.train | tail -n 1 | awk '{print \$5}' | tr '\\n' '\\t' >> ${prefix}.train.tsv
+    # Do not take the last 'substitution percent identity' value; it is calculated from a matrix rounded to integers
+    grep 'substitution percent identity' ${prefix}.train |
+        tail -n 2 | head -n 1 | awk '{print \$5}'                                        | tr '\\n' '\\t' >> ${prefix}.train.tsv
     grep 'last -t' ${prefix}.train | tail -n 1 | awk '{print \$2}'   | sed -e 's/-t//'   | tr '\\n' '\\t' >> ${prefix}.train.tsv
     grep 'last -a' ${prefix}.train | tail -n 1 | awk '{print \$3}'                       | tr '\\n' '\\t' >> ${prefix}.train.tsv
     grep 'last -A' ${prefix}.train | tail -n 1 | awk '{print \$3}'                       | tr '\\n' '\\t' >> ${prefix}.train.tsv

modules/nf-core/last/train/tests/main.nf.test.snap

@@ -70,7 +70,7 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.train.tsv:md5,a2fca4aabda82f0aa481085ce5258886"
+                        "contigs.train.tsv:md5,c8721d9cabf1e2b7c0d2d3dac9ed3db8"
                     ]
                 ],
                 "2": [
@@ -82,7 +82,7 @@
                             "id": "contigs",
                             "single_end": false
                         },
-                        "contigs.train.tsv:md5,a2fca4aabda82f0aa481085ce5258886"
+                        "contigs.train.tsv:md5,c8721d9cabf1e2b7c0d2d3dac9ed3db8"
                     ]
                 ],
                 "param_file": [
@@ -101,8 +101,8 @@
         ],
         "meta": {
             "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nextflow": "25.04.8"
         },
-        "timestamp": "2025-03-10T11:02:48.369194"
+        "timestamp": "2025-10-20T14:56:15.004824885"
     }
 }