Feature Request: Add --subdirs flag to obtain directory output for MultiQC compatibility

[hemant-goyal]

Context:
Currently, when running Falco on multiple local files with a single output directory (-o), Falco intelligently prefixes the output filenames to prevent overwriting (e.g., sample_name_R1_fastqc_data.txt or/and sample_name_R2_fastqc_data.txt).

However, downstream parsers like MultiQC strictly mandate the exact filename fastqc_data.txt to successfully ingest the data. Because of the prefixing, MultiQC fails to recognize bulk local Falco outputs unless the user writes a custom wrapper script to isolate each run into its own folder.

Proposed Feature:
Introduce a --subdirs flag. When this argument is passed, Falco would automatically create a sample-specific subdirectory for each input file inside the target -o directory, placing the standard fastqc_data.txt inside it.

Benefit:
This would perfectly mimic FastQC's default directory-creation behavior, making Falco 100% out-of-the-box compatible with MultiQC for bulk local runs without requiring users to write custom bash loops.

(Split from issue #38 as requested).

[andrewdavidsmith]

I think this needs a bit more clarification. You seem to be suggesting that this "Falco intelligently prefixes the output filenames to prevent overwriting", while desirable, might not be the best way to go. I don't see a --subdirs arg in fastqc, so I need a bit more info. I'll look into it myself eventually, but if you can answer it would accelerate things.

[hemant-goyal]

I wanted to clarify exactly why this is the missing puzzle piece for pipeline integration.

Currently, when passing multiple files to a single -o directory, Falco intelligently prefixes the filenames (e.g., sample_name_fastqc_data.txt) to prevent them from overwriting each other. However, MultiQC's internal search_patterns.yaml strictly mandates that the FastQC module only triggers on files named exactly fastqc_data.txt or *_fastqc.zip. During my previous testing with Falco, I explicitly followed this method.

By implementing --subdirs, Falco would organize the batch into sample-specific folders out-of-box, allowing the output files to retain the exact fastqc_data.txt name. This will make Falco natively compatible with MultiQC for bulk local runs without users needing to write custom bash wrappers to isolate the files or custom search configurations.