Unexpected behaviour when using seq option multiple times

[mbhall88]

The -1/-i/--seq option takes the fastq file(s) to be analysed by mykrobe. This option can be used multiple times or just solo. However, I discovered that if it is used multiple times, only the last occurence is used. For example

• -1 in.fq: uses in.fq
• -1 in.fq in2.fq: uses in.fq and in2.fq
• -1 in.fq -1 in2.fq: uses in2.fq only

[iqbal-lab]

Wot

[martinghunt]

Just being picky, but the help does say to use the option once, not more than once ;) That said, it does make sense to allow of your 3 examples

[mbhall88]

Fair. Well we would either need to error if it is used twice, or allow it then I guess...