Support for Read Lengths Not in {50, 100, 150, 200}

Description of the bug

Hello,

I am using the nf-core/atacseq pipeline and need to specify the --read_length parameter for my FASTQ files, which have a read length of 76 bp. However, the pipeline currently only allows --read_length values of 50, 100, 150, or 200, making it unclear how to proceed with read lengths that fall outside these values.

According to the documentation, the --read_length parameter is used to define the --sjdbOverhang parameter in STAR as (read_length - 1), which is critical for accurate alignment. For my case, the correct sjdbOverhang should be 75, but there is no direct way to specify this in the pipeline.

Proposed Solutions

1. Allow Users to Directly Specify sjdbOverhang

   • Introduce a new optional parameter (e.g., --sjdbOverhang) that lets users override the value instead of relying on --read_length.

2. Expand --read_length Options

   • Instead of restricting --read_length to specific values, allow users to input any valid read length.

3. Auto-Detect Read Length from Input FASTQs

   • The pipeline could infer the read length from the input FASTQ files and set sjdbOverhang accordingly.

Would it be possible to implement one of these solutions in a future release? Let me know if there's any workaround in the meantime.

Thanks for your help!

Command used and terminal output

Relevant files

No response

System information

No response

No files or tests are identified. Start by locating the --read_length parameter definition and the STAR invocation, then determine which proposed approach the maintainers want to support. Done means a 76 bp input can configure sjdbOverhang as 75, with coverage for the supported parameter behavior.