write stdout+stderr to autotax_log.txt

KasperSkytte · Jun 30, 2021 · c3384f8 · c3384f8
1 parent 729d2c7
commit c3384f8
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Showing 2 changed files with 10 additions and 7 deletions.
diff --git a/autotax.bash b/autotax.bash
@@ -1,5 +1,5 @@
 #!/usr/bin/env bash
-export VERSION="1.6.1"
+export VERSION="1.6.2"
 
 #################################
 ############# setup #############
@@ -224,15 +224,19 @@ derep() {
 
 denoise() {
   #check user arguments
+  local minsize=2
   local OPTIND
-  while getopts ":i:o:" opt; do
+  while getopts ":i:o:s:" opt; do
     case ${opt} in
       i )
         local input=$OPTARG
         ;;
       o )
         local output=$OPTARG
         ;;
+      s )
+        local minsize=$OPTARG
+        ;;
       \? )
         userError "Invalid Option: -$OPTARG"
         exit 1
@@ -245,8 +249,7 @@ denoise() {
   done
   # Denoise with UNOISE3 accepting sequences seen only twice (see article supplementary for why this is acceptable)
   echoWithHeader "  - Denoising sequences using UNOISE3"
-  usearch11 -unoise3 $input -zotus $output -minsize ${denoise_minsize}
-  #cp temp/uniques_wsize.fa temp/preFLASVs.fa
+  usearch11 -unoise3 $input -zotus $output -minsize $minsize
 }
 
 findLongest() {
@@ -1278,7 +1281,7 @@ then
     esac
   done
   shift $((OPTIND -1))
-  autotax
+  (autotax) |& tee autotax_log.txt
   if [ $? -gt 0 ]
   then
     exit 1

diff --git a/tests.bats b/tests.bats
@@ -71,7 +71,7 @@ load autotax
 	[ "$status" -eq 0 ]
 
 	#check if output pattern matches the format " *** [2020-03-16 10:08:30]: test"
-	pattern="^ *** \[[0-9\ -:]*\]: test$"
+	pattern="^ \*\*\* \[[0-9\ -:]*\]: test$"
 	[[ ${lines[0]} =~ $pattern ]]
 }
 
@@ -186,7 +186,7 @@ load autotax
 	[ "$status" -eq 1 ]
 
 	#expect no error
-	run denoise -i $in -o ${test_run_dir}$out
+	run denoise -i $in -o ${test_run_dir}$out -s 2
 	echo $output >&2 #redirect to stderr for debugging
 	[ "$status" -eq 0 ]