docs for samtools_reheader

sanger-tol · Jun 28, 2024 · c6568fe · c6568fe
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diff --git a/docs/output.md b/docs/output.md
@@ -79,6 +79,10 @@ The filtered PacBio reads are aligned with `MINIMAP2_ALIGN`. The sorted and merg
 
 ## Alignment post-processing
 
+### External metadata
+
+If provided using the `--header` option, all output alignments (`*.cram`) will include any additional metadata supplied as a SAM header template, replacing the existing *@HD* and *@SD* entries (note that this behaviour can be altered by modifying the `ext.args` for `SAMTOOLS_REHEADER` in `modules.config`.
+
 ### Statistics
 
 The output alignments, along with the index, are used to calculate mapping statistics. Output files are generated using `SAMTOOLS_STATS`, `SAMTOOLS_FLAGSTAT` and `SAMTOOLS_IDXSTATS`.

diff --git a/docs/usage.md b/docs/usage.md
@@ -66,6 +66,9 @@ work                # Directory containing the nextflow working files
 # Other nextflow hidden files, eg. history of pipeline runs and old logs.
 ```
 
+You can also optionally supply a template SAM header using the `--header` option to add or modify metadata associated with the assembly, which will be incorporated into the output alignments.
+
+
 ### Updating the pipeline
 
 When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: