Releases: tgen/phoenix
Releases · tgen/phoenix
phoenix_v1.2.0
New Features
- bcftools stats for each caller #366
- Support for fasterq
- Metrics workflow
- New PCR-free workflows #384
- Illumina expansion hunter
- Constitutional gatk_cnv
- Very similar to the tumor only workflow
- tHReD workflow #432
CMD Changes - Will cause restarts
- Cellranger has been updated to v6.0.1, includes updated changes for fastq naming and expected number of cells #403, #166
- Updated md5sum bam/cram generation for better pathing #425
- stats2json and stats2lims workflow fix for bam level jsons #418
- Only will cause restarts for bam_qc_all jsons
- Summarize_mm_igtx will now have a constant number of columns depending on the number of callers and genes #415
- mm_igtx_gammit
- Updated workflow to reduce variability in alignments and updated script for processing the assembled bam
- Fixed output of annotSeg.pl to properly header the seg.vcf file and give proper calcuation for the SVLEN
Task flow changes
- Modified fastq tracking for salmon, no change in render though
phoenix_v1.1.2
Minor release focusing on bug fixes
CMD Changes - Will cause restarts
- The bed files used for mutation burden have been updated with respect to vep and snpeff, previous results had the chance to count the same mutation more than once, increasing the perceived mutation burden.
- Part of the chip workflow (spike_in_calibration) has been updated to fix some syntax errors as well as setting a floor for the scaling when creating the bed graph.
phoenix_v1.1.1
New Features
- RSEM is now available.
CMD Changes - Will cause restarts
- Mutation Burden has an updated tool version (v1.2.3) and now we set the filtering options during the render, we are using the same values as the defaults, but this is better for visibility.
- Star_quant will now place the *.Log.final.out into the respective stats directory. #406
- The script(s) for pairoscope have been consolidated into one script and have updated regions that are filtered. #388
Task flow changes
- We have updated the remove files macro to allow for generically defined naming, previously it would always use the task name that it was dependent on. This is being used for better workflow setup after star_quant tasks are completed.
- Pairoscope is now using a study level defined variable for setting the --call_requirement option. We also by default set this to 4.
Other changes
- Renamed cds_intervals to canoncical_cds_intervals.
phoenix_v1.1.0
New Features
- Tumor only workflow
- Built using callers from the somatic workflow as a blueprint.
- Requires a user defined normal bam and/or panel of normals depending on which tasks are enabled.
- Contains an assembly based workflow which we refer to as gammit, the fasta generated from this process is available in the results directory. #390
- Utilizes a tumor only specific version of pairoscope. #261, #363
- lumosVar2 support has been added #81
- Metrics workflow
- Adds tgen_mutation_burden calculation
- Adds msisensor_pro support
- snpsniffer_summary is now completely operational.
CMD Changes - Will cause restarts
- Bcftools annotate update, adding TOPMED, and providing more valuable information into the annotations, such as the AC as reported by the annotation database.
- ichorCNA updates #385
- No longer uses the default panel of normals (PoN), as this led to the loss of data on chr17. Now the PoN is user defined and should be tailored to your samples.
- We now set --normalizeMaleX FALSE, as this caused unexpected results for chrX.
- We added support for the tumor fraction and ploidy values to be uploaded to LIMS.
- Mutect2 and octopus will restart due to a combination of improper linkage to the removing_files task and an update to their inputs to include the tbi file.
- stats2json and stats2lims updates which support:
- Samtools_stats - summarize_samstats.R update which fixes edge case bugs related to positions being exactly equal to the expected position and updates for coverage percentile calculations.
- manta_prepare_sv_vcf.py has been updated to fix edge case bugs when a variants position is close to the edge of a chromosome.
- Star alignment output has been updated and will now output *.Log.final.out which contains parsable data. #392
- gatk_collecthsmetrics now uses a coverage cap of 2000. #389
- ig_ENST_filter path has been updated to fix a typo, this will cause salmon to restart.
Task flow changes
- For almost all variant callers (deepvariant, freebayes, genotypegvcf, haplotypecaller, lancet, mutect2, octopus, strelka2, vardict), we did not specify that the vcf index file was an input, this has been fixed now. If using smart copy from jetstream_centro then this change causes a minimum number of restarts, e.g. only performs the filtering process again. It does not cause the caller to restart entirely.
- add_matched_rna will now reset vcfmerger2 when necessary.
Other changes
- Fixed the naming usage of cutrun glpreps for chip gltypes.
- mm_igtx_pairoscope moved from the constitutional module directory to tumor only directory.
- gatk_collectrnaseqmetrics has a minor logic update to ensure a bash if statement is rendered.
- stats2json now has a lims_upload true/false argument.
- Updated reference of reference_non_N_bed to reference_non_N_interval_list in the pipeline.yaml as the file is 1-based (interval_list), not 0-based (bed).
phoenix_v1.0.2
This release is not backwards compatible with v0.x.x pipeline results
This version is not backwards compatible with previous versions. Previous results need to be deleted before the use of a v1.x.x pipeline. If you do not remove the previous results, there will be two tasks attempting to copy the same fastq, due to a copy fastq task name change.
Minor release update containing bug fixes related to task flow and a handful of code changes.
CMD Changes - Will cause restarts
- Updated constitutional and somatic octopus workflows to include a sort after vcf chunk concatenation, fixing odd cases where the calls are out of order in the concatenated vcf.
- Star-fusion inspector has a slight modification for counting the number of fusions, previously we would trigger an exit if 0 fusions were found.
- Lancet now implements a cleaner and slightly faster approach for fixing the vcf output from lancet.
- Samtools_stats - summarize_samstats_*.R has had a version change which fixes edge case bugs related to positions being exactly equal to the expected position vs being greater than.
Task flow changes
- We fixed potential race conditions related to haplotypecaller tasks and a hovering remove files task.
- In the main.jst for qc, we were missing the taskPrefix for one of the calls to sex_check.
- Major overhaul for star_quant tasks post mark duplicates. We can now submit many after tasks into the remove files macro. Meaning that we can have the remove files wait for any combination of htseq, featurecounts, and fixmate_sort.
Other changes
- Copy fastq no longer will submit to the isilon partition as it will be removed at a later date.
phoenix_v1.0.1
This release is not backwards compatible with v0.x.x pipeline results
This version is not backwards compatible with previous versions. Previous results need to be deleted before the use of a v1.x.x pipeline. If you do not remove the previous results, there will be two tasks attempting to copy the same fastq, due to a copy fastq task name change.
Minor release update containing pairoscope and star-fusion changes. Updated required scripts readme with script locations.
CMD Changes - Will cause restarts
- Updated mm_igtx_pairoscope_calling_b38.py to the latest version and fixed numLines call in mm_igtx_calling.jst
- star-fusion has a new cp in place for copying an intermediate file to be used later with fusion validator
phoenix_v1.0.0
This release is not backwards compatible with previous pipeline results
This version is not backwards compatible with previous versions. Previous results need to be deleted before the use of a v1.x.x pipeline. If you do not remove the previous results, there will be two tasks attempting to copy the same fastq, due to a copy fastq task name change.
New Features
- Converted tasks to use input/output where possible in anticipation of cloud usage
- Jetstream reset utilization for any task that uses inputs from a temporary space
- Removed the usage of PATH_TO_PHOENIX_REPO, in favor of Jetstream JS_PIPELINE_PATH
- Chip-Seq support has been added #285
- All tasks within primary workflows have been profiled and now have optimized resource allocation calls
- Copy number vcf support #326
- md5sum generation for bam to cram #320
CMD Changes - Will cause restarts
- Copy fastq task naming
- Previous implementation used a simple iterative approach, which results in potential task mixups when new data was added. The new implementation ensures data stability between each run, but this will result in all projects needing to restart from scratch
- RNA changes
- Single Cell changes
- Cellranger
- Added a bam reheader step, cellranger defaults to 0.1 for the library. Since we know the library from the project configuration we replace this value
- Added bam to cram and bam qc
- Star Solo
- Output file naming adjustments
- Added bam qc
- Cellranger
- Copy Number Updates #309
- QC Updates
- Somatic changes
- Constitutional changes
- Set call requirement to 4 within mm_igtx_calling #319
- Ichor_cna now merges the output pdfs into a minimal set
- Numerous tool version updates
- bcftools and htslib - 1.10.2
- deepvariant - 0.10.0
- gatk - 4.1.8.0
- htseq - 0.12.3
- multiQC - 1.9
- salmon 1.2.1
- star 2.7.5a
Other Changes
- Moved utility tasks to their own macros/jsts #338
- Moved and renamed external scripts within the required_scripts directory
phoenix_v0.5.0
New Features
- Initial support for jetstream 1.6 features, now tasks that require fastqs will reset their predecessors if they get reset. Meaning that we now support the addition of new fastq data during potential project restarts.
- Deepvariant now generates g.vcfs.
CMD Changes - Will cause restarts
- Updated deepvariant to 0.9.0
- Added support for g.vcfs
- Updated deepvariant models
- IchorCNA now moves one additional file to the results directory
- Adjusted constitutional manta threading (was calling for 38 threads before, but only given 20)
- Star-Fusion now uses samtools sort when keeping the BAM
- Star-Fusion uses an updated index with Gencode v32
- RNA variant check now echos to the proper vcf spec (Description needed quotes)
Other Changes
- Added reset predecessors to tasks that use fastqs as an input
phoenix_v0.4.3
This is a minor developmental release that fixes some potential bugs when using manta, primary changes are:
- Swapped manta/1.6-GCCcore-8.2.0 with manta/1.6, the GCCcore-8.2.0 version runs into odd bugs with high coverage data
- Delly now uses the openMPI module and is now "sample" threaded, meaning that is uses two threads during somatic variant calling. This speeds up variant calling and can potentially allows some instances to get past the split-read alignment step and reach completion
phoenix_v0.4.2
CMD Changes - Will cause restarts
- The gatk collect metrics tasks now include --java-options to set the behavior we expect from gatk-java
Other Changes
- Re-optimized gatk metrics memory usage