Comments (4)
alimanfoo
commented on September 11, 2024
Hi folks, given that dockerfiles might be reused across multiple pipelines, shall we put these in a root level /dockerfiles directory in this repo?
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tnguyensanger
commented on September 11, 2024
Sure. We have a whole bunch of dockerfiles used in PF7 and for general cromwell/sanger access testing under: https://gitlab.com/malariagen/gsp/executor/-/tree/master/Docker.
We can move them over.
I'm sure the NIHR amplicon sequencing folks have their own set of docker files.
from pipelines.
JonKeatley112
commented on September 11, 2024
The Dockerfiles i moved to executor are the ones from amplicon
from pipelines.
alimanfoo
commented on September 11, 2024
Cool, thanks @tnguyensanger, @JonKeatley112. The specific versions of the tools we need are in the spec.
from pipelines.
Related Issues (20)
- Provide example crams released by Core Sequencing HOT 3
- Define read group contents in vector short read alignment pipelines HOT 1
- Input source for mosquito short read alignment pipeline HOT 3
- Validation/truth datasets for variant calling calibration, comparison and evaluation HOT 26
- Copy script to convert vcf to zarr to this repo
- Port baseline Plasmodium amplicon SNP calling pipeline. HOT 1
- Add platform argument to build_pipeline_release script HOT 2
- How to make bwa short read alignment deterministic for testing HOT 1
- Mosquito phasing pipeline development HOT 22
- Genotype Concordance Validation of genotyping pipelines HOT 10
- Create pipelines that download multiple samples from IRODS in a batch
- Determine final lanelet manifest fields required for vector alignment and genotyping HOT 1
- Cromwell configurations on farm5 are using localization = copy, which explodes size of workflow working directory
- Convert cram to bam in vector alignment pipeline
- malaria-dk lsf group deprecated
- Output of vector short read alignment pipeline is named *.bam.bam HOT 1
- Use flexible fields in manifest
- Validate results for phasing pipeline HOT 17
- Ag3.0 phasing pipeline production run HOT 15
- Number of SNPs and Indels doesn't match with the numbers reported in README files HOT 4
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