Provide additional customisation options during init step for generation of the config file

[ahfitzpa]

I would like to use LACA for shorter amplicons (600 bp) from ONT sequencing.

Can you provide the following options in the laca init so that the config file can work with alternative sequence input?

• amplicon length
• fw_primer
• rev_primer

[yanhui09]

Thanks for interesting in LACA.
laca init is actually wrapped cmd to generate the snakemake config.yaml. There are many variables in config file, so at this moment I only include as commonly used ones as cmd arguments. Like fw_primer or rev_primer, some users may have multiple sets, so it's a bit hard to be integrated in the arguments. But any time you can edit the config.yaml file which is generated by laca init.

I have referenced to lines to adjust primers and amplicon length

amplicon length:

laca/laca/workflow/config_template.yaml

Lines 38 to 39 in 2af0f0e

	min_len: 800
	max_len: 1500

fw/rev_primer:

laca/laca/workflow/config_template.yaml

Lines 44 to 51 in 2af0f0e

	fprimer:
	27Fa: "AGAGTTTGATYMTGGCTYAG"
	27Fb: "AGGGTTCGATTCTGGCTCAG"
	338Fa: "ACWCCTACGGGWGGCAGCAG"
	338Fb: "GACTCCTACGGGAGGCWGCAG"
	rprimer:
	1540R: "TACGGYTACCTTGTTACGACT"
	1391R: "GACGGGCGGTGTGTRCA"