tempe_v1.2.2

Minor patch

Bugfixes:

• Set snpSniffer to default to false instead of true, this means that if all tasks are disabled or missing in the config we will only run the default alignment with bwa
• Fixed input/output for bcftools annotate - previously the annotation databases were considered as outputs, not inputs
• Shifted deepvariants dynamic memory allocation to be ~16G higher per bin, which is less prone to OOM kills in our testing
• Adjusted constitutional manta to place output files in the results_dir a bit earlier, which is better for downstream processing
• Added prepare_tumor_only resets to the tumor only variant callers that did not have this set already
• Omitting a denylist region within chunk4 of the calling intervals, this region is prone to significant walltime runouts #65
• Bumped to discordant_loci_extractor v0.1.6 to fix errors when input volume/data is low

Improvements:

• Configured tumor_only sigprofiler to use a more strictly filtered vcf, which yields comparable results to the somatic sigprofiler output
• Updated stats2lims to handle lane level stats #55

Full Changelog: v1.2.1...v1.2.2

tempe_v1.2.1

Minor patch

Bugfixes:

• Fixed usage of externally defined variables, they previously required an all or nothing approach to the definitions.
• Fixed a copy-paste typo for constitutional GATK CNV which resulted in the tasks not rendering/running. #51
• Regression bugfix from v1.2.0: v1.2.0 introduced a bug for the usage of scripts that exist within the pipeline/repo wherein the render would unintentionally update for certain tasks due to pathing changes for the pipeline's install location. Resulting in wasted compute. Fortunately these tasks are usually lightweight. This bugfix works best with Jetstream v1.7.4, but it's possible to use older Jetstream versions if some workarounds are in place.

Improvements:

• Bumped deepvariant to v1.6.0 - this reportedly has improved performance for the NovaSeqX. Additionally this allows us to multithread the postprocess_variants task. The postprocess_variants task does require more memory in our testing.
• Added filters to PASS for constitutional Manta, and we've added annotation via VEP. #52

Full Changelog: v1.2.0...v1.2.1

tempe_v1.2.0

Feature Release

Major changes (Changes that cause restarts are in bold):

• All containers have been updated to use a more optimimally sized image, or using the image provided by the authors

  • We changed base containers over to debian instead of a heavy rockylinux base, also moved to multi-stage builds
• Tool updates for bcftools, samtools, htslib, deepvariant, GATK, ichorCNA, sigprofiler, vardict
• We have added support for user supplied variables for the variant filtering tasks
• New tools added:
  • CNVear
  • b_pure
• Added PCR Free workflow #15
• Since alignment must restart, #17 is handled
• Adjusted support for fasterq files #24
  • Petagene is only loaded for the copy fastq step and is decompressing the fasterq as part of the copy operation
• Multiple UMI aware alignment updates #25 #26 #27 #36 #37
• Adjusted memory usage for a couple of workflows including lancet and deepvariant #33
  • Deepvariant is using an example of memory request based on the numberOfReads in the sample, this is planned to be expanded upon
• CPU usage tuning #40 #43 #44
• DeepVariant edge case bugfix #42
• VEP pick order updated and adding --mane annotation #41
• Removed workflows that are outdated/superseded by newer tools:
  • snpEff
  • singleCellRNA support tasks (these will be broken into a separate pipeline in order to reduce workflow complexity)
  • lumosVar
  • CHIP/CutRun alignment and processing

This update will cause all tasks to restart based on the container changes, and we apologize for the inconvenience, it is technically possible to avoid this if jetstream is told
to not include the container and digest as part of the task identity, rerender the workflow, and set tasks back to their previous state. Then mash the workflow with the new tempe
version. A lot of tasks will still restart as a result of this, but you might be able to avoid restarting back to the alignment steps. This operation is not recommended, but feel
free to contact bturner@tgen.org for assistance if this is required for your work.

Full Changelog: v1.1.2...v1.2.0

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You must use Jetstream v1.7.3+ in order to run this pipeline
This is due to some additional template functions that have been added to the pipeline, namely an md5 function to render the md5sum of a file at render time, and assignBins, which is used to create and assign user defined bins.

tempe_v1.1.2

Minor Patch

Bug Fixes:

• FusionInspector has been broken out to a separate task similar to how we've run things in previous pipelines - previous implementation generated FusionInspector results, but due to naming differences, these results were not landing in the results_dir - This will cause restarts with RNA
• Moved expansion hunter to only run for normals and slight reorganization of constitutional main
• md5sum_bam_cram output pathing fixes, important for smart copy
• Edge case bugfix for vcfMerger - bump to v0.9.4 - vcfMerger tasks will want to restart
• SigprofilerAssignment bugfix to handle cases where DINUC matrices are not generated

Features:

• Resolving #6 - as requested back in the phoenix pipeline

Full Changelog: v1.1.1...v1.1.2

Important note

Additional features/bugfixes are expected soon for a v1.2.0 release - Most of these are multiple myeloma focused, but as a preview we will be resolving #15 and #17, enabling the mm_igtx workflows, etcetera. A major note is that v1.2.0 will cause restarts by nature of resolving #15 and #17, part of this addition is the move to samtools v1.17

tempe_v1.1.1

Minor patch

A very minimal update, simply adding {{ directory }} to the task input for the removing_files task. This ensures that this directory is mounted when running with the jetstream slurm_singularity backend. This will not cause any restarts.

Full Changelog: v1.1.0...v1.1.1

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You must use Jetstream v1.7.x in order to run this pipeline

This release is not backwards compatible with previous phoenix pipeline results

This version is not backwards compatible with previous versions. This should only be used for "fresh starts". E.g. if you have a new project. Any task of the same name will be reset as we've moved to using container based workflows.

tempe_v1.1.0

Feature Release

Major changes (Changes that cause restarts are in bold):

• More consistent {{ temp_dir }} and {{ results_dir }} usage
• Tool updates for mutation_burden, vcfmerger, freebayes
• Changed over to default tasks to false instead of true
  • This saves on time if people are running the pipeline without setting tasks to true, e.g. if they submit a config that only enables a few tasks, then we shouldn't try to run things not mentioned in the config. This also maintains that task control naming is consistent.
• CHIP variant filtering
• SigprofilerAssignment implementation
• Umi alignment updates
• Tumor Only workflow adaptation/updates

This update will cause a lot of tasks to restart, though in many cases the actual tool versions, CLI options, etc. have not changed. Most tasks will restart due to an output location change which is required for consistent paths between temp and results directories as well as avoids clobbering files if more than one aligner is selected. While not recommended in most cases, it's possible to update existing task renders and move files to their newer destinations. Please reach out to bturner@tgen.org for assistance.

Full Changelog: v1.0.1...v1.1.0

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You must use Jetstream v1.7.x in order to run this pipeline

This release is not backwards compatible with previous phoenix pipeline results

This version is not backwards compatible with previous versions. This should only be used for "fresh starts". E.g. if you have a new project. Any task of the same name will be reset as we've moved to using container based workflows.

tempe_v1.0.1

Patch Release

Relatively minor changes here:

• Now using vcfmerger 0.9.1 to resolve bug in strelka prep
• Removing files macro update to have more intricate before directive logic, allows for placing before multiple tasks instead of just one
• Minor cleanup in dna_alignment main

This should only cause restarts for vcfmerger as the before directive is not part of the task identity.

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You must use Jetstream v1.7.x in order to run this pipeline

This release is not backwards compatible with previous phoenix pipeline results

This version is not backwards compatible with previous versions. This should only be used for "fresh starts". E.g. if you have a new project. Any task of the same name will be reset as we've moved to using container based workflows.

tempe_v1.0.0

Initial Release

This pipeline is designed to use container images only and has dropped the usage of module loads. This allows the pipeline to be much more portable. Additionally we have bumped the versions of tools used for many tasks and streamlined the task options available based on usage.

You must use Jetstream v1.7.x in order to run this pipeline

This release is not backwards compatible with previous phoenix pipeline results

This version is not backwards compatible with previous versions. This should only be used for "fresh starts". E.g. if you have a new project. Any task of the same name will be reset as we've moved to using container based workflows.