diff --git a/README.md b/README.md
index c5c06be..ba9de7c 100644
--- a/README.md
+++ b/README.md
@@ -101,7 +101,7 @@ CD-Hit clusters
 | --dssp	| Map DSSP code to alignment 	 | false | 	 | 
 | --squeeze	| Squeeze alignment towards conserved 2nd structure categories | false	 | "H,E" |
 | --squeezePerc	| Set minimal occurence % of anchor element in MSA 	 | 80	 |  |  
-| --reorder	| Order final MSA by input file order 	| false	 | "gamma.fasta,delta.fasta” <br>  “true” for alphabetical order  | 
+| --reorder	| Order final MSA by input file order 	| false	 |  | 
 | --convertMSA	| Covert final MSA file from fasta to selected file format	| 	false |  "clustal" | 
 | --magic	| Launch a run with recommended settings for all parameters	 | false	 |  | 
 
@@ -448,7 +448,7 @@ see [above](#mappingissues)
 ## 8. Reorder MSA (--reorder)
 Output: `results/outFolder/reordered_*_merged_finalmsa_alignment.fasta`
 
-- Order MSA according to the order of sequences in the input files in alphabetical order or by user defined order **--reorder "gamma.fasta,delta.fasta”**
+- Order MSA according to the order of sequences in the input files. If more then one sequence input file is provided, order MSQ based on the order given in the files organized alphabetically. Instead of alphabetically, can also select explicitly how to organize the files with **--reorder "gamma.fasta,delta.fasta”**
 
 ## 9. Convert MSA 
 Output: `results/outFolder/seqs/converted_*_merged_finalmsa_alignment.fasta`
diff --git a/magic_hydra.sh b/magic_hydra.sh
index a505565..62aeb6c 100755
--- a/magic_hydra.sh
+++ b/magic_hydra.sh
@@ -1,5 +1,6 @@
 #!/bin/bash
 #screen -S nextflowalign bash -c ./magic_hydra.sh
+
 data=toy_example
 
 module load Nextflow/23.04.2
@@ -9,7 +10,8 @@ output_name=${data}_${now}_test
 output_folder=$house/results/$output_name
 mkdir -p $house/results
 mkdir -p $output_folder
-nextflow run simsapiper.nf -resume \
+
+nextflow run simsapiper.nf \
     -profile hydra \
     --data $house/$data/data \
     --magic \