All notable changes to this project are documented in this file.
- ProgramTarget in genairics.targets and ProgramDependencyBase in ##genairics.tasks, for program dependencies.
- --cluster-PPN option for qsub job-launcher to specify number of processors per node to request.
- Created genairics.targets, genairics.tasks and genairics.config.
- coverageTask to RNAseq pipeline to generate bw coverage file. this also sorts the bam and creates its index for visualization in a genome browser.
- Moved a lot of code out of genairics.init into the more relevant submodules targets, tasks and config
- setupProject and ProjectTask offer getLogger method.
- Example hello world script for external pipelines.
- Starting through qsub no longer worked because of changed bool flag arguments. Preparing qsub env variables and reading them fixed.
- setupLogging deprecated
- External pipelines in genairics CLI through env variable GAX_PIPEX.
- processSamplesIndividually task that acts as a checkpoint reference task for sample results merging task that can be agnostic of the sample specific processing task.
- pairedEnd processing operational.
- CLI bool arguments can now simply be provided as a flag,
e.g.
--pairedEnd, and not--pairedEnd Trueas was required before.
- merging of FASTQs no longer at project level but at sample level. Unmerged FASTQs are no longer moved to _original_FASTQs subfolder. The merged FASTQ are put in the result sample subfolder. By default they are deleted after the singel sample processing steps, as by then usually only the bam files are required.