Get error message when using Directory as workflow input: "Input Directory contains unusable symlink"
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zzzseeu commented
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:
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
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!