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

By default, the nfcore/rnaseq 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:

`--saveAlignedIntermediates`
The final BAM files created after the Picard MarkDuplicates step are always saved
and can be found in the `markDuplicates/` folder.
Specify this flag to also copy out BAM files from STAR / HISAT2 alignment and sorting steps.

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

`--saveReference`
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.saveReference = true
params.saveTrimmed = true
params.saveAlignedIntermediates = true

For more help, see the following documentation:

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