Merge pull request #253 from wtsi-npg/devel

merge from devel to master to create release 0.24.1

Changes

@@ -1,5 +1,7 @@
 CHANGES LOG
 -----------
+release 0.24.1
+ - correct count of minimum reads to run Salmon
 
 release 0.24.0
  - allow format selection for stage1 outputs/stage2 inputs (default: cram)

data/vtlib/salmon_alignment.json

@@ -99,14 +99,14 @@
 					"--geneMap", {"subst":"annotation_val", "required":"yes"},
 					"--output", {"subst":"salmon_out"},
 					{"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-p", {"subst":"b2c_mt_val"} ]}}}, "\";",
-					"case `file $0` in *ASCII*) PART1=`head -c 50K $0 | wc -l`;; *compressed*) PART1=`gunzip -c $0 | head -c 50K | wc -l`;; *empty*) PART1=0;; esac;",
+					"case `file $0` in *ASCII*) PART1=`head -n 1000 $0 | wc -l`;; *compressed*) PART1=`gunzip -c $0 | head -n 1000 | wc -l`;; *empty*) PART1=0;; esac;",
 					"if [[ $0 && ! $1 ]]; then",
 						"SALMON_CMD+=\"-r $0\";",
 						"if [[ $PART1 -lt 1000 ]]; then",
 							">&2 printf \"Not enough reads to run Salmon: fq: %s\" \"$((PART1/4))\"; exit 0; fi;",
 					"elif [[ $0 && $1 ]]; then",
 						"SALMON_CMD+=\"-1 $0 -2 $1\";",
-						"case `file $1` in *ASCII*) PART2=`head -c 50K $1 | wc -l`;; *compressed*) PART2=`gunzip -c $1 | head -c 50K | wc -l`;; *empty*) PART2=0;; esac;",
+						"case `file $1` in *ASCII*) PART2=`head -n 1000 $1 | wc -l`;; *compressed*) PART2=`gunzip -c $1 | head -n 1000 | wc -l`;; *empty*) PART2=0;; esac;",
 						"if [[ $PART1 -lt 1000 || $PART2 -lt 1000 ]]; then",
 							">&2 printf \"Not enough reads to run Salmon: fq1: %s - fq2: %s\" \"$((PART1/4))\" \"$((PART2/4))\"; exit 0; fi; fi;",
 					"$SALMON_CMD'",