Update Running-the-Pipeline-batch.md

add a warning that input file in -gwascatalog model will be deleted

docs/Tutorials/Running-the-Pipeline-batch.md

@@ -48,7 +48,9 @@ nextflow run EBISPOT/gwas-sumstats-harmoniser \
 -with-trace \
 -profile executor,singularity
 ```
-
+:::warning
+The `--gwascatalog` option will automatically delete the input file and any intermediate files, retaining only the final result in the FTP folder. Please ensure that the files in the all_harm_folder are copies.
+:::
 ## Handling Multiple Files in One Job
 When running multiple files in one Nextflow job, the pipeline is designed to ignore errors generated by individual files. If a file encounters an error, its process will halt, but it will not affect the progress of other summary statistics in the same job. Since different files may progress at different rates, we recommend using the `-with-trace` option to generate a trace file. This allows you to monitor the progress of each file individually.
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