mtandon09 / CCBR_GATK4_Exome_Seq_Pipeline

An easy-to-use, flexible variant calling pipeline for use on the Biowulf cluster at NIH

https://mtandon09.github.io/CCBR_GATK4_Exome_Seq_Pipeline/

MIT License

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Incorporating QC docker images #8

Closed skchronicles closed 3 years ago

skchronicles commented 3 years ago

Changelog

Adding option to config to specify tmp directory or local node storage
Adding functionality to resolve docker/singularity bind paths in configs
Updating following rules in qc.smk to use docker images:
- fc_lane
- fastqc
- fastq_screen
- kraken + krona
- qualimap
- multiqc