# Grouping outputs into separate directories

**URL:** <https://cwl.discourse.group/t/grouping-outputs-into-separate-directories/965>\
**Category:** CWL Questions\
**Created:** [December 10, 2024, 7:44pm UTC](https://cwl.discourse.group/t/grouping-outputs-into-separate-directories/965 "2024-12-10T19:44:51Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![skgo](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@skgo](https://cwl.discourse.group/u/skgo)\
**Post date:** [December 10, 2024, 7:44pm UTC](https://cwl.discourse.group/t/grouping-outputs-into-separate-directories/965/1 "2024-12-10T19:44:51Z")

</div>

Is there a straightforward way to group outputs from specific steps into different output directories? For example, say my workflow is something like trim → align → call variants → qc. I would like to group the results (and possibly intermediates) from each of those steps into separate directories with a structure like:

```auto
trim
    - SAMPLE-ID
        - Fastq1
        - Fastq2
alignment
    - SAMPLE-ID
        - Final bam
        - Intermediate bam
vc
    - SAMPLE-ID
        - Final VCF
        - Intermediate VCF
qc
    - SAMPLE-ID
        - Trim QC report
        - Align QC report
        - Variant QC report

```

I’m aware of the `--leave-outputs` option but that isn’t quite what I want. I’m transitioning from Nextflow to CWL and this output structure is very simple to achieve in Nextflow. I’m wondering if I’m overlooking some documentation for CWL that discusses this.