# Attempting to stage multiple files into a directory **URL:** \ **Category:** CWL Questions\ **Created:** [March 30, 2026, 4:32pm UTC](https://cwl.discourse.group/t/attempting-to-stage-multiple-files-into-a-directory/1044 "2026-03-30T16:32:09Z")\ **Posts on this page:** 5\ **Page:** 1
**Author:** ![skgo](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@skgo](https://cwl.discourse.group/u/skgo)\ **Post date:** [March 30, 2026, 4:32pm UTC](https://cwl.discourse.group/t/attempting-to-stage-multiple-files-into-a-directory/1044/1 "2026-03-30T16:32:09Z")
I am attempting to pass in multiple files as inputs and stage those specific files into a directory, which is provided as a named input to my tool. Specifically, this is for hisat2. I am unable to provide them up front in a directory due to other limitations not related to CWL or hisat2. Here is an example of how I’ve constructed the folder: ```auto requirements: InlineJavascriptRequirement: {} InitialWorkDirRequirement: listing: - entryname: "hisat2_index" entry: | ${ return { "class": "Directory", "listing": [inputs.hisat2_idx_1, inputs.hisat2_idx_2, inputs.hisat2_idx_3, inputs.hisat2_idx_4, inputs.hisat2_idx_5, inputs.hisat2_idx_6, inputs.hisat2_idx_7, inputs.hisat2_idx_8] }; } ``` And here is how I am attempting to use it: ```auto arguments: - prefix: -x valueFrom: hisat2_index ``` I have also tried: ```auto arguments: - prefix: -x valueFrom: $(runtime.outdir)/hisat2_index ``` In both cases I receive the error `(ERR): "hisat2_index" does not exist` or `(ERR): "/vBrQqO/hisat2_index" does not exist` respectively. Is there something I’m missing? ---
**Author:** ![davidjsherman](https://yyz2.discourse-cdn.com/free1/user_avatar/cwl.discourse.group/davidjsherman/32/205_2.png) [@davidjsherman](https://cwl.discourse.group/u/davidjsherman)\ **Post date:** [April 1, 2026, 8:14am UTC](https://cwl.discourse.group/t/attempting-to-stage-multiple-files-into-a-directory/1044/2 "2026-04-01T08:14:02Z")
I find it easier to specify the directory base name in the returned Directory object. ```auto requirements: InlineJavascriptRequirement: {} InitialWorkDirRequirement: listing: - |2 ${ var asset = { basename: "hisat2_index", class: "Directory", listing: [ inputs.hisat2_idx_1, inputs.hisat2_idx_2, inputs.hisat2_idx_3, inputs.hisat2_idx_4, inputs.hisat2_idx_5, inputs.hisat2_idx_6, inputs.hisat2_idx_7, inputs.hisat2_idx_8 ], writable: false }; return asset; } ``` ---
**Author:** ![skgo](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@skgo](https://cwl.discourse.group/u/skgo)\ **Post date:** [April 1, 2026, 5:58pm UTC](https://cwl.discourse.group/t/attempting-to-stage-multiple-files-into-a-directory/1044/3 "2026-04-01T17:58:50Z")
How exactly do I reference that directory? When I use your changes and run with the `--debug` flag it appears that the directory is correctly being created: ```auto DEBUG [job hisat2.cwl] initial work dir { "_:40d2c1d0-92eb-4686-a1be-67c81157d6c9": [ "_:40d2c1d0-92eb-4686-a1be-67c81157d6c9", "/CkSeWc/hisat2_index", "Directory", true ], ``` and I do see it being populated with files: ```auto "file:///my_input_path/hg38.1.ht2": [ "/my_input_path/hg38.1.ht2", "/CkSeWc/hisat2_index/hg38.1.ht2", "File", true ], ``` However, when I try to use that directory like so: ```auto arguments: - prefix: -x valueFrom: $(runtime.outdir)/hisat2_index ``` I get the error: ```auto (ERR): "/CkSeWc/hisat2_index" does not exist ``` ---
**Author:** ![skgo](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@skgo](https://cwl.discourse.group/u/skgo)\ **Post date:** [April 2, 2026, 4:49pm UTC](https://cwl.discourse.group/t/attempting-to-stage-multiple-files-into-a-directory/1044/4 "2026-04-02T16:49:02Z")
I’ve done some test runs keep the tmpdir for inspection and am having trouble making sense of the results. When I run with a container image I see it’s mounting the tmpdir like so: ```auto --mount=type=bind,source=/tmp/fx8xwvn0,target=/LqxIIY ``` and when I `ls /tmp/fx8xwvn0` I see that hisat2\_index exists and is populated as expected. However, I am getting the error `(ERR): "/LqxIIY/hisat2_index" does not exist`. It seems to me that based on the mounting that that path should exist. I’ve also tried running this without a container to attempt to diagnose if this is just a container specific issue. When I do that I see ```auto INFO [job hisat2.cwl] /tmp/hh3_owur$ hisat2 \ -x \ /tmp/hh3_owur/hisat2_index \ -k \ 1 \ -1 \ /tmp/sp2h1bwd/stg4906f7cd-d64d-4d88-bbaa-35df80ba6f2c/tmp_r1.fq \ -2 \ /tmp/sp2h1bwd/stgae1e9627-dafa-4298-9c13-c65f1da4c329/tmp_r2.fq \ -S \ aligned.sam (ERR): "/tmp/hh3_owur/hisat2_index" does not exist ``` but I can run `ls /tmp/hh3_owur/hisat2_index` and see that it does exist and is populated with all of the files as expected. ---
**Author:** ![skgo](https://avatars.discourse-cdn.com/v4/letter/s/7cd45c/32.png) [@skgo](https://cwl.discourse.group/u/skgo)\ **Post date:** [April 2, 2026, 7:46pm UTC](https://cwl.discourse.group/t/attempting-to-stage-multiple-files-into-a-directory/1044/5 "2026-04-02T19:46:35Z")
I swapped to using this ```auto requirements: InitialWorkDirRequirement: listing: - entryname: hisat2_index/hg38.1.ht2 entry: $(inputs.hisat2_idx_1) - entryname: hisat2_index/hg38.2.ht2 entry: $(inputs.hisat2_idx_2) - entryname: hisat2_index/hg38.3.ht2 entry: $(inputs.hisat2_idx_3) - entryname: hisat2_index/hg38.4.ht2 entry: $(inputs.hisat2_idx_4) - entryname: hisat2_index/hg38.5.ht2 entry: $(inputs.hisat2_idx_5) - entryname: hisat2_index/hg38.6.ht2 entry: $(inputs.hisat2_idx_6) - entryname: hisat2_index/hg38.7.ht2 entry: $(inputs.hisat2_idx_7) - entryname: hisat2_index/hg38.8.ht2 entry: $(inputs.hisat2_idx_8) ``` and it’s working now. I’m not entirely sure why, but at least it’s working now. Perhaps I had a typo somewhere.