Closed Mxrcon closed 2 years ago
which could be fixed by updating the multiqc to the latest version (v.1.12), we should check this update as it'll downgrade the picard version to 2.17, this shoudn't be a problem as the bioconda recipe for mtbseq requires picard >=2.17.0.
So, what's the picard version in the env as of now?
So, what's the picard version in the env as of now?
Using conda env export
: picard=2.27.1=hdfd78af_0
Cool, then I think that we're good to go 🤞
Thanks Davi!
Hey, :wave: as requested on our latest meeting and mentioned in https://github.com/mtb-bioinformatics/mtbseq-nf/pull/58#issuecomment-1112037563. I'm giving some attention to the qc_reports workflow.
I tried to run the pipeline normally without specifying --skip-qc so I could check if the qc report is working as normal.
I got this error message:
This error was throw because of differences into the
fastqc
outputs andmultiqc
inputs, so I emitted a new named channel so they'll match.After that The version of multiqc was giving a odd error:
which could be fixed by updating the multiqc to the latest version (v.1.12), we should check this update as it'll downgrade the picard version to 2.17, this shoudn't be a problem as the bioconda recipe for mtbseq requires picard >=2.17.0.
runing
MTBseq --check
:After those changes, I started to run mtbseq_nf again to double check if the changes into the conda env would make any change.
Happy to contribute with this work, feel free to add changes or request any modification on my approach to the errors.
Kindly, Davi