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Input naming conventions
Follow up to https://github.com/nf-core/modules/pull/1437#discussion_r834774713
We currently use reads
for unaligned reads(fastq
), and then bam
for the aligned reads, but this doesn't cover cram
, and sam
.
It also doesn't cover things like when a bam
or a bed
file are possible.
I personally think input
is a little too vague to name the variable as well.
as mentioned in the other PR I like
aligned_input
or input_aligned
for bam/cram/sam and then aligned_index
for bai/crai/sai
as usual @FriederikeHanssen is right on point
For modules that download a database, a naming convention would be great.
I've seen download
, update
, and setupdb
. But I also understand some of these might actually be the names of the subcommand to download the database (e.g. amrfinder_update
)
I don't know what effect #1338 might have on this, but it might solve some of it.