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MHH-RCUG / Wochenende

Deprecated see https://github.com/MHH-RCUG/nf_wochenende : A whole Genome/Metagenome Sequencing Alignment Pipeline in Python3
https://github.com/MHH-RCUG/nf_wochenende
MIT License
37 stars 16 forks source link

conda env improvements, testing, plot srun speedup #154

Closed colindaven closed 3 years ago

colindaven commented 3 years ago
poer-sophia commented 3 years ago

I tried to create a new wochenende env with your new yaml but I got this error: solving environment: failed resolvepackagenotfound: - multiqc-1.11-pyhdfd78af_0

So I deleted the line with multiqc in the yml, created the enviroment and then installed multiqc with conda install -n wochenende-c bioconda -c conda-forge multiqc

Multiqc worked with this env for me. Could ou try if you can create the enviroment from this new yaml?

colindaven commented 3 years ago

This sounds promising, we'll have to get Ilona to try it as well. It works for me, great.

colindaven commented 3 years ago

Hey, the bam.txt files are just our metagenomics file. A bam.bai (index) file belongs to every bam file. I've reverted in the next commit to dev.

poer-sophia commented 3 years ago

But I need the bam.txt files to get the length of the sequence for every organism. I guess it is the simplest way to get it.