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Update Running-the-Pipeline-batch.md
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jiyue1214 authored Oct 31, 2024
1 parent b793b6b commit 118cae1
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4 changes: 2 additions & 2 deletions docs/Tutorials/Running-the-Pipeline-batch.md
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Expand Up @@ -31,7 +31,7 @@ nextflow run EBISPOT/gwas-sumstats-harmoniser \
--harm \
--list to_harmonise_files_list.txt \
-with-trace \
-profile cluster,singularity \
-profile executor,singularity \
```

## Harmonising files from a folder
Expand All @@ -44,7 +44,7 @@ nextflow run EBISPOT/gwas-sumstats-harmoniser \
--ref $ref \
--all_harm_folder $all_harm_folder \
-with-trace \
-profile cluster,singularity
-profile executor,singularity
```
## 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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