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Hello development team,
thank you for providing such a convenient tool. I encountered the following problem when using it, and I hope to get your help.
I want to use Directory as an input parameter in the workflow. My code is as follows:
Directory
input
workflow
version development workflow fastp_workflow { input { String output_prefix Directory in_dir } call fastp { input: read1 = "${in_dir}/test_R1.fastq", read2 = "${in_dir}/test_R2.fastq", output_prefix = output_prefix } output { File trimmed_read1 = fastp.trimmed_read1 File trimmed_read2 = fastp.trimmed_read2 File html_report = fastp.html_report File json_report = fastp.json_report } } task fastp { input { File read1 File read2 String output_prefix } command { fastp \ -i ${read1} \ -I ${read2} \ -o ${output_prefix}_1.fastq \ -O ${output_prefix}_2.fastq \ --html ${output_prefix}.html \ --json ${output_prefix}.json } output { File trimmed_read1 = "${output_prefix}_1.fastq" File trimmed_read2 = "${output_prefix}_2.fastq" File html_report = "${output_prefix}.html" File json_report = "${output_prefix}.json" } runtime { docker: "quay.io/biocontainers/fastp:0.23.4--h125f33a_5" } }
My input json file likes:
{ "fastp_workflow.in_dir": "/mnt/e/ISH/biocompute-platform/miniwdl-test", "fastp_workflow.output_prefix": "trimmed_sample" }
Then I run miniwdl using command: miniwdl run -i input.json fastp.wdl
miniwdl run -i input.json fastp.wdl
But it returns an error:
Input Directory contains unusable symlink: /mnt/e/ISH/biocompute-platform/miniwdl-test
My miniwdl version is v1.12.1.
Can you please tell me how to solve this problems?
Looking for your reply. Thanks again!
The text was updated successfully, but these errors were encountered:
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Hello development team,
thank you for providing such a convenient tool. I encountered the following problem when using it, and I hope to get your help.
I want to use
Directory
as aninput
parameter in theworkflow
. My code is as follows:My input json file likes:
Then I run miniwdl using command:
miniwdl run -i input.json fastp.wdl
But it returns an error:
My miniwdl version is v1.12.1.
Can you please tell me how to solve this problems?
Looking for your reply. Thanks again!
The text was updated successfully, but these errors were encountered: