Open Sanaz01 opened 6 days ago
glob feature to capture all files with similar pattern is not working on PROOF/ Cromwell. Here are the inputs and outputs:
glob
Input WDL: glob_test.wdl
glob_test.wdl
workflow GlobTest{ input{ String name_list } call make_files{ input: names=name_list } output { Array[File] = outfiles = make_files.output_files } } task make_files{ input { String names } command <<< set -eo pipefail IFS=',' for name in ${names} do echo ${name} >> file_${name}.txt done; wait >>> runtime { docker: "ubuntu:noble-20240114" cpu: "1" memory: "1 G" } output{ Array[File] output_files = glob("file_*.txt") } }
Input Json: glob_test.json
glob_test.json
{ "GlobTest.name_list": "Harry,Sally,Tammy" }
Error in Troubleshoot tab in PROOF
[1] "Could not process output, file not found: /hpc/temp/paguirigan_a/user/sagarwa2/cromwell-scratch/GlobTest/736d876b-3673-4f9d-a9ce-81c7693b3dd5/call-make_files/execution/glob-d667704679d03197544d1107735ba61b/file_*.txt"
Thanks @Sanaz01 Does it work when you don't use PROOF?
@sckott I have not tested this WDL workflow via command line.
okay, thanks. I'll see what I can find out
glob
feature to capture all files with similar pattern is not working on PROOF/ Cromwell. Here are the inputs and outputs:Input WDL:
glob_test.wdl
Input Json:
glob_test.json
Error in Troubleshoot tab in PROOF