Dev replikation

[replikation]

• living PR on code rewrite and test profiles

[hoelzer]

@working guppy CPU #20 I can test this if you want (do we have some test fast5 somewhere, OSF?)

[replikation]

-profile test_fast5 @hoelzer see help; fastq fasta and fast5 can be "auto supplied" for testing

[hoelzer]

-profile test_fast5 @hoelzer see help fastq fasta and fast5 can be "auto supplied" for testing

ah, awesome! I will test!

btw you switched to V1200 primer set as the default now? (its fine, just to know because e.g. P3 uses V3 currently)

[replikation]

V3 should be the default; its only set to V1200 for the test fastq set (as i only had a good and small one for V1200)

[hoelzer]

V3 should be the default; its only set to V1200 for the test fastq set (as i only had a good and small one for V1200)

ah, I see. great!

[replikation]

• @hoelzer i would merge now

[hoelzer]

@replikation looks good!

• I just updated president
• and I switched from baseName to simpleName for fastq input because otherwise I ended up with something like FAO96286_barcode07.fastq_seq_ident_check.tsv because baseName did not remove the .fastq from a .fastq.gz file