Skip to content

Add lack of support for auto-detection from stdin to the docs #658

@mikemc

Description

@mikemc

Running fastp from STDIN, whether interleaved paired data with --detect_adapter_for_pe, or on single-end data, runs with no error but outputs messages that auto-detection is disabled (example below). It would be helpful to note this behavior in the README and doc string.

cat test_interleaved.fq | fastp \
  --stdin \
  --interleaved_in \
  --detect_adapter_for_pe \
  --json report_stream.json \
  --html report_stream.html
Adapter auto-detection is disabled for STDIN mode
Adapter auto-detection is disabled for STDIN mode
Read1 before filtering:
...

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions