=====================
 Where are my files?
=====================

By default, the nf-core/methylseq pipeline does not save large intermediate files to the
results directory. This is to try to conserve disk space.

These files can be found in the pipeline `work` directory if needed.
Alternatively, re-run the pipeline using `-resume` in addition to one of
the below command-line options and they will be copied into the results directory:

`--unmapped` (bismark only)
Specify to save FastQ files containing reads that didn't map to the reference genome to the results directory.

`--save_align_intermeds`
The final BAM files created after the Bismark deduplicate / Picard MarkDuplicates steps are always saved
and can be found in the `bismark_deduplicated/` or `bwa-mem_markDuplicates/` folder, respectively.
Specify this flag to also copy out BAM files from bismark / bwameth alignment and sorting steps.

`--save_trimmed`
Specify to save trimmed FastQ files to the results directory.

`--save_reference`
Save any downloaded or generated reference genome files to your results folder.
These can then be used for future pipeline runs, reducing processing times.


-----------------------------------
 Setting defaults in a config file
-----------------------------------
If you would always like these files to be saved without having to specify this on
the command line, you can save the following to your personal configuration file
(eg. `~/.nextflow/config`):

params.save_reference = true
params.save_trimmed = true
params.save_align_intermeds = true
params.unmapped = true

For more help, see the following documentation:

https://github.com/nf-core/methylseq/blob/master/docs/usage.md
https://www.nextflow.io/docs/latest/getstarted.html
https://www.nextflow.io/docs/latest/config.html
