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nf-core / bamtofastq

Converts bam or cram files to fastq format and does quality control.
https://nf-co.re/bamtofastq
MIT License
21 stars 13 forks source link

Documentation and things #4

Closed FriederikeHanssen closed 4 years ago

FriederikeHanssen commented 4 years ago

This may be subject to change as it requires some discussion with @ggabernet on how we want to do this.

FriederikeHanssen commented 4 years ago

I think we should merge this, there are too many changes in this PR overall. We can discuss the header and logos etc outside of this PR

FriederikeHanssen commented 4 years ago

@matrulda added a bit to the docu. Feel free to correct everything I am not explaining well. Also haven't gotten around to the output yet.

matrulda commented 4 years ago

Cool cool! Just at first glance: there are a lot of new files. Looks like a lot of result files, I guess they were committed by mistake?

FriederikeHanssen commented 4 years ago

oh shoot! Not sure how that happened. Will remove them

matrulda commented 4 years ago

Awesome work @FriederikeHanssen ! Looks very good to me. Only have one question, right now the empty bam isn't used as far as I can see. Is the plan to include it in a test later?

FriederikeHanssen commented 4 years ago

Yes that would be the plan, to catch empty or corrupted files but run the others through. I haven't figured out how to do this yet and report back to the user. Maybe I can somehow use errorStrategies for that

matrulda commented 4 years ago

Yeah, maybe the error code for "corrupt/empty bam" can be assigned the ignore strategy. I'm unsure how it will play out downstream though.

But so for this PR, I think it would be more clean to not include that file until is used in a test. But since this is WIP anyway,I'm fine with merging if you'd like to keep it.

FriederikeHanssen commented 4 years ago

You are right. Will remove it here and merge, if that is good for you. Probably better to add this as issue so I won't forget it later

matrulda commented 4 years ago

Yes, sound good! 👍