conflicting advice in usage document

[sansense]

Description of the bug

In methylseq v4.1.0 noticed something unclear in the documentation. In the main usage guide under Parameters, it states:

“It is mandatory to provide --fasta along with --bismark_index / --bwameth_index parameters.”

However, on the detailed parameter page (https://nf-co.re/methylseq/parameters/), it says:

“If the aligner is Bismark and bismark_index is specified, this parameter is ignored.”

That second description is consistent with older releases I’ve used (e.g., v1.6.1), where a FASTA file was never required unless something had changed in Bismark. So I’m unsure whether the requirement in the v4.1.0 usage guide is accurate.

Command used and terminal output

Relevant files

No response

System information

No response

[sateeshperi]

will update the docs. thanks