Charlie

@evolphotonics I notice `force_overwrite` is false, I wonder if setting that to true would achieve the desired effect of automatically overwriting intermediate files. Unfortunately I'm not sure there's anything to...

Great, thanks for the reply. I'm going to close this issue, please open a new one if this kind of behavior is observed in sunbeam3.

Closing this as it should work in sunbeam3. If you encounter this again please open a new issue.

Can this issue be closed? This should work in sunbeam3 (other than that one version where I broke it).

I run sunbeam3 on WSL2 (Ubuntu 20.04.3 LTS) and have never run into this issue. In the interest of cleaning up all these megahit issues from version

Closing this issue as it should be fixed in sunbeam3. If you run into this again please open a new issue.

Hi Michael, These lines are actually pretty deceptive because of some of the weird data structures used. I'm just gonna start by listing out data types of everything involved then...

Are all of those fields necessary to uniquely identify each sample? i.e. do your files look like this: 1_A_1_1_R1.fastq, 1_A_1_1_R2.fastq, 2_A_1_1_R..., 2_A_2_1_R..., 2_A_2_2_R..., ... or like this: info_A_1_123_R1.fastq, info_A_1_123_R2.fastq, info_B_1_123_R1.fastq,...

What happens when you run `sunbeam init --data_fp /path/to/files /project/fp` on these?

Hi Michael, I'm going to close out this issue. I'd advise just using the default pattern matching from `sunbeam init --data_fp` and if you need to rename products that's easy...