seqkit replace incorrectly uses the '-i' flag

[ammaraziz]

Have you checked the docs?

• nf-core website: troubleshooting
• nf-core modules documentation

Description of the bug

The seqkit replace module incorrectly uses the -i flag, I think the intended usage was to specify the input (incorrect). The -i is --ignore-case. Seqkit uses positional argument to specify the input.

It should be removed from here:

modules/modules/nf-core/seqkit/replace/main.nf

Lines 33 to 38 in 04dcc4d

	seqkit \\
	replace \\
	${args} \\
	--threads ${task.cpus} \\
	-i ${fastx} \\
	-o ${prefix}.${endswith}

It's not the end of the word, but it may break some peoples code. It should however still be removed as case is important.