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HISTORY
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HISTORY
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0.67 New single-step bam indexing pipeline. New Conifer pipeline. New
retroseq pipeline. Improved breakdancer pipeline. The vrpipe datasource
now has an option to filter after grouping. The vrtrack_auto_qc pipeline
now always fails a lane if the NPG status was failed. When a submission
fails and is retried, the stdout/err of previous attempts is now
accessible, eg. with vrpipe-submissions.
0.66 vrpipe-setup can now be used to change pipeline behaviours.
0.65 New breakdancer pipeline, single-step bam splitting pipeline, and the
vrpipe datasource now applies the filter after grouping, requiring only
1 file in the group to match the filter.
0.64 Fix for bam_reheader, affecting 1000 genomes pipelines.
0.63 Fix for rare bug in fastq_split which prevented it from working with
certain input.
0.62 Critical fix for new queue switching code.
0.61 Now, if a job is running in a time-limited queue, and the limit is
approaching, the job will be switched to a queue with a longer time
limit.
0.60 Fix for vrpipe-setup to make it compatible with the new vrtrack_auto_qc
pipeline.
0.59 New vrtrack_auto_qc pipeline. New (alternate) SNP pipeline. New
vrpipe-permissions script.
0.58 Various fixes to enable initial install and testing for new users using
latest CPAN modules.
0.57 vrpipe-fileinfo can now tell you how a file was generated.
0.56 New gatk_variant_calling_and_filter_vcf pipeline.
0.55 Further merge pipeline fixes. New bam realignment around discovered
indels pipeline.
0.54 Further fix for new merge pipeline.
0.53 Fixed issues with bam merging pipelines, and renamed tham all.
0.52 New fofn_with_metadata DataSource - useful for inputting external bams
into pipelines. VRTrack-releated steps now have
deadlock-failure-avoidance.
0.51 VRTrack DataSource now has an option to group_by_metadata.
0.50 New merge_bams pipelines, to do "merge across". VRTrack datasource now
allows filtering on more status types, and can get VRPipe improved bams.
0.49 Critical bug fix in bam_to_fastq step.
0.48 Tweaks and fixes to finalise new bam_genotype_checking pipeline.
0.47 Minor tweaks to finalise yet-unused pipelines.
0.46 New versions of merge lanes and stampy mapping pipelines with extra
features.
0.45 Critical speed fix for vrtrack datasource. Library merge pipelines now
index the resulting bams.
0.44 Fix for plot_bamcheck step, letting it work when then is no insert size.
0.43 Efficiency fix for vrtrack datasource.
0.42 Critical fix for vrtrack datasource, so that it now updates file
metadata when vrtrack metadata changes.
0.41 vrtrack_update_improved step now sets lane reads and bases.
0.40 Critical fix for vrtrack_update_mapstats step, letting it work without
exome_targets_file.
0.39 vrpipe DataSource behaviour changed, so that a child pipeline that
deletes inputs won't mess up a parent that still needs those files.
Overhauled the genotype checking pipeline and steps.
0.38 Fix for gatk_target_interval_creator step, increasing its default memory
reservation.
0.37 Overhaul of qc graphs & stats-related steps and pipelines so that now
wgs and exome projects all use the same pipeline, with a single bamcheck
call. bam_to_fastq step fixed so that it runs in constant <500MB and
copes with bams that miss reads.
0.36 Critical fixes to the underlying system to ensure job submission doesn't
stall out forever, to handle limits on steps better, and to avoid issues
when there are multiple submissions for the same job. Also a fix for
java to increase likelyhood of jvm starting up.
0.35 vrpipe-status script improved to give a better overview of what the
pipeline is doing, with warnings about pipeline stalls. bam_to_fastq
step reimplemented, should now be much better.
0.34 Critical speed fix for the VRTrack datasource. Fixes for the
archive_files pipeline and the vrtrack_update_mapstats step.
0.33 Optimised bam_import_from_irods_and_vrtrack_qc_wgs pipeline. Memory and
time reserved for jobs is now less likely to be insufficient.
0.32 Fixes for bam_mapping_with_bwa_via_fastq and bam_reheader step.
Efficiency improvement in how step max_simultaneous is handled.
0.31 Database independence now properly implemented. New separate bam
improvement pipeline, remapping bams via fastq pipeline, and some
Sanger-specific pipelines added.
0.30 Fixes related to archive_files pipeline.
0.29 New archive_files pipeline.
0.28 Really fix java-using steps so they get the memory they need.
0.27 Outputs of near-identical PipelineSetups will now never risk overwriting
themselves. Java-using steps get better recommended memory. New
IMPORTANT_NOTES file - you must read this!
0.26 Critical performance fix for StepStats.
0.25 New StepStats system for quick access to memory/time used stats.
0.24 Critical fix for mapping pipeline.
0.23 New Stampy mapping pipline. Fixes for SNP and DCC pipelines.
0.22 Critical fix for input files that are relative symlinks.
0.21 SNP discovery pipeline(s) now firming up; fixes for merging pipelines
0.20 Improved handling of limits, so that a good amount of jobs are always
running.
0.19 Various fixes to 1000 genomes-related pipelines.
0.18 Fix to allow sqlite to be used in production.
0.17 Install process for new external users should now work/be easy.
0.16 New merging pipelines and associated vrpipe datasource (for chaining
different pipelines together). Critical bug fixes that allow changes in
datasources to trigger restarts for the changed elements.
0.15 Front-end for creating PipelineSetups; improvements to smalt mapping so
we can map 454 data in 1000 genomes.
0.14 More front-end scripts added. Sequence index datasource now starts.
changed elements over from scratch, so we can now change the source file
safely.
0.13 Various fixes for pipelines. Memory leak issues fixed. Various front-end
scripts added.
0.12 Fixes for bam_mapping_with_bwa. New VCF annotation-related steps and
pipelines. Triggering pipelines in Manager has been optimised slightly.
0.11 Fixes for bam_mapping_with_bwa. New smalt mapping pipeline for handling
454 sequence data.
0.10 Bam Improvement steps now fully implemented. New bam_mapping_with_bwa
pipeline.
0.09 Scheduler independence: local can now be used for testing.
0.08 Submission retries now add time where necessary.
0.07 Fixed critical bug in mapping pipeline; should now work properly.
0.06 Myriad performance and stability improvements necessary to get the
mapping pipeline running smoothly.
0.05 Critical performance fix for dealing with large datasources.
0.04 Critical performance fix for checking bam file type.
0.03 0.02 only worked on test dataset; this should be the first version to
work on real data, following important schema changes and Step fixes.
0.02 Most interesting features not yet implemented, but this is the first
working version, needed to do the 1000genomes phase2 (re)mapping.
0.01 No real files; just starting up repository.