Releases: ucsd-ccbb/C-VIEW
Releases · ucsd-ccbb/C-VIEW
4.1.0
Fixes bugs and tweaks outputs, including:
- Removes --analysis-mode fast from pangolin call so it uses usher (by default)
- Adds sequencing_tech and sample_sequencing_datetime fields to qc_and_lineages summary file * (and downstream reports)
- Changes "stringent" condition to use "overall_fail" (more exclusive) rather than "any_fail"
- Changes logging to include stdout instead of just stderr
- Adds retry for AWS downloads because of intermittent failures
- Fixes search-and-replace error where "qc" was replaced by "src"
4.0.1
- Fix typo preventing aggregation of pi metrics at QC step
- Add more detail about cluster creation to README.md
4.0.0
Major release:
- Change from SGE scheduler to Slurm scheduler to support AWS ParallelCluster version 3
- Update installation script and conda environment yaml, including
- Upgrade to
pi_from_pileup
version 1.0.3 - Install iVar via
conda
- Upgrade to
- Update and extend README.md with detail on installation and cluster creation
- Update folder structure and script names for better usability
- Output full
*pi_from_pileup.tsv
for each sample in addition to*pi-metric.tsv
3.9.0
- Sets
Ready for release?
value toNo
in bjorn-ready file for any sample with known bad metadata - Generates md5 checksums for each run's
*-passQC.fas
and*-summary.csv
file during QC step - Creates a file of the md5 checksums of each
*-passQC.fas
and*-summary.csv
file used as input during the lineage identification step- Copies of each
*-passQC.fas
and*-summary.csv
are no longer uploaded to the S3 output, to reduce duplication and storage use
- Copies of each
- Removes creation of no-longer-used
passQC
output folder during lineage identification - Refactors confusing code in custom stats generation QC step
3.8.0
- Adds ability to input bams produced by Genexus instrument instead fastqs
- Adds
variants_qc
functionality that runs both per-sample processing and QC summarization for single sequencing run - Corrects bug in which
Pct >=Q30
value for single-end reads was output as fraction instead of percent - Corrects bug in which
uncapped_reads_lt_100k
metric was actually calculated as uncapped_reads < 50k - Modifies QC metric calculations to account for metrics that are missing because they cannot be calculated from bam inputs.
- A missing metric is no longer treated as a False value for that metric; metrics are now allowed to be True, False, or None
- None values are ignored when calculating logical combinations such as
any_fail
(except in the case where ALL metrics are None, in which case the logical combination of them is treated as False).
3.7.0
- Updates sample names in unit tests to follow naming convention
- Moves regression test files out of this project
- Moves helper scripts out of this project
3.6.0
Support for pangolin 4+ :
- Adds
--analysis-mode fast
to pangolin call to continue to use pangoLEARN as classifier - Removes consensus sequence munging no longer used in pangolin 4+
- Updates expected of status column name in pangolin output
As of this release, C-VIEW is not compatible with pre-4.0 pangolin versions. This should not be a problem as C-VIEW automatically updates pangolin to the latest on every run, so there should be no case in which it is attempting to run an older version.
3.5.0
- Removes tree-building and visualization functionality (now performed externally)
- Includes stand-alone
update_files_w_iqtree_renames.py
script to update alignment and metadata files with IQ-TREE-munged sequence names (to support insertion of new sequences into an IQ-TREE-created base tree) - Documents
cumulative_pipeline
function - Adds
-J
option tosamtools depth
to exclude deletions from coverage calculations - Excludes samples with negative ages from bjorn file
3.4.1
- Updates git repo link and conda environment names in install.sh
- Explicitly deactivates pangolin environment and reactivates main C-VIEW environment after pangolin use in lineages.sh
- Removes code to support "loose" samples subset processing in lineages.sh
3.4.0
Modifies creation of bjorn summary to:
- add a column containing the bam s3 url
- prevent an error if no samples are eligible for bjorn
- mark a sample as ready for release if it has overall_fail = False and has new metadata column submit_to_gisaid = True (this should prevent e.g. CDPH sample inclusion)
- add the state abbreviation into the virus name
Modifies tree prep to:
- define "stringent" samples as those with any_fail = False (instead of usable_for = variant_and_epidemiology)
- cease creating metadata and fas files for "loose" samples (such are no longer defined)