ampliconsuite-pipeline - v1.3.9

• update for AC v1.4.1
• enforce CNVkit NUMEXPR_MAX_THREADS to be same as user-specified value
• samtools sort threads will not exceed user-specified threading value
• bugfix to setting of rscript path before calling CNVkit batch
• move data repo recency timing check earlier
• extend flexibility of graph_cleaner.py
• docker runscript checks if given fastqs actually exist before sending to docker run command
• logging improvements

- Python
Published by jluebeck 9 months ago

ampliconsuite-pipeline - v1.3.8

• bugfix for edge case where --no_filter and CNV generation are set
• logging tweaks
• Released with updated AC v1.3.3

- Python
Published by jluebeck 10 months ago

ampliconsuite-pipeline - v1.3.7

• Makes python3 explicit in subprocess calls
• Packaged with AC v1.3.2, AA v1.5.r2

- Python
Published by jluebeck 10 months ago

ampliconsuite-pipeline - v1.3.6

• GroupedAnalysisAmpSuite.py: Bugfix to launching jobs with threads < samples.
• Warn if Mosek license expiring soon
• Released with AA v1.5.r1, AC v1.3.1

- Python
Published by jluebeck 11 months ago

ampliconsuite-pipeline - v1.3.5

• Add ability to provide SV VCF column in GroupedAnalysisAmpSuite.py input file for each sample individually.
• Add some warnings for grouped analysis if input file is formatted incorrectly.
• Expose --pair_supportmin and `--foldbackpairsupportminarguments from AA toAmpliconSuite-pipeline.py`. These are exposed in the Docker & Singularity runscripts too.
• Release with AA v1.5.r0.

- Python
Published by jluebeck about 1 year ago

ampliconsuite-pipeline - v1.3.4

• clean up temporary reference fasta when matched normal given
• fix logging of AA version when python2 used
• clear previous run logfile when launching a rerun (previously would append to end of previous log)
• bugfix to GroupedAnalysis when multiple normal samples given

- Python
Published by jluebeck over 1 year ago

ampliconsuite-pipeline - v1.3.3

AmpliconSuite-pipeline 1.3.3

• Accompanies AmpliconClassifier 1.2.0 and AmpliconArchitect 1.4.r2 updates
• fix bug in GroupedAnalysisAmpSuite.py where not all samples analyzed if number of threads is smaller
• add checking of exit codes from subprocesses in GroupedAnalysisAmpSuite.py
• require user to provide location of .sif file for Singularity usage.
• lazy loading of some libraries so that --download_repo can be used without installing any dependencies
• improvements in logging

- Python
Published by jluebeck over 1 year ago

ampliconsuite-pipeline - v1.3.2

AmpliconSuite-pipeline 1.3.2

• Accompanies AC v1.1.4 update
• reduce_fasta.py is now integrated as a library file, not a script
• improved error messages about mosek license
• rename intermediate file pre_filtered.bed to unfiltered_gains.bed and put in cnvkit directory to avoid confusion about its contents.

- Python
Published by jluebeck almost 2 years ago

ampliconsuite-pipeline - v1.3.1

• Remove bloat from container images (Docker 8.7GB -> 2.2GB. Singularity 6.0GB -> 636MB)
  • This was due to unnecessary, massive pytorch GPU packages being included with CNVkit's dependencies by default.
• Remove bloat from standalone installer script (pytorch GPU packages)
• Add bedtools as a dependency
• GroupedAnalysisAmpSuite.py will automatically compute feature similarity scores.
• GroupedAnalysisAmpSuite.py bugfix when CNV seeds are already provided in input table.
• GroupedAnalysisAmpSuite.py detect improperly formatted input table.
• Automatically detect samtools version (removes --use_old_samtools)
• Warn user if alt contigs in bam header.
• Fix logging of AA version in run_metadata.json.
• Better protection for bad inputs (e.g. user gave same fastq twice, bam file with spaces in name)
• Fix no amp samples not getting ref genome version in run_metadata.json
• Update Rscript package installation in containers.
• Bugfix to manual specification of Singularity image file location

- Python
Published by jluebeck almost 2 years ago

ampliconsuite-pipeline - v1.2.2

• Bugfix to GroupedAnalysisAmpSuite.py when matched normal not included
• Distributable packages to include v1.3.r8 of AmpliconArchitect
• Distributable packages to include v1.1.2 of AmpliconClassifier

- Python
Published by jluebeck about 2 years ago

ampliconsuite-pipeline - v1.2.1

• Bugfix in AmpliconClassifier

AmpliconSuite-pipeline version incremented for re-packaging.

- Python
Published by jluebeck about 2 years ago

ampliconsuite-pipeline - v1.2.0

• adds --download_repo option so users can obtain data repo files using AmpliconSuite-pipeline.py
• update install.sh
• conda recipe update for AC 1.1.0
• documentation updates and logging tweaks

- Python
Published by jluebeck about 2 years ago

ampliconsuite-pipeline - v1.1.3

• Bugfixes to handling of CNV seeds file when using GroupedAnalysisAmpSuite.py
• Update for AA v1.3.r7

- Python
Published by jluebeck about 2 years ago

ampliconsuite-pipeline - v1.1.2

• debug linkage with AmpliconClassifier for conda-installed versions of AmpliconClassifier
• minor changes to docs and logging
• add manifest.in

- Python
Published by jluebeck about 2 years ago

ampliconsuite-pipeline - v1.1.1

• Bugfix to finding AmpliconClassifier when installed via conda.
• Minor tweaks to logging, docs

- Python
Published by jluebeck about 2 years ago

ampliconsuite-pipeline - v1.1.0

• update conda recipe for AmpliconClassifier version 1.0.0, which adds ecDNA context reporting
• Update documentation in GUIDE.md
• Bugfix to GroupedAnalysisAmpSuite.py invokation of AmpliconSuite-pipeline.py
• improve install.sh --finalize_only when docker or singularity is used (thanks Owen Chapman)
• add test output files to compare against in test_outputs/ directory
• add script to get timing log get_AA_log_timing.sh from multiple samples to help evaluate runtime on large batches of samples
• add script to evaluate how commonly specific regions end up in seed files from a collection of bed files seed_overlap_counts.sh
• fix behavior of --no_filter
• --sv_vcf arg in docker and singularity uses absolute path of file

- Python
Published by jluebeck over 2 years ago

ampliconsuite-pipeline - v1.0.0

1.0.0 is here! Not because of huge new improvements to the pipeline in this release, but because the features and codebase are finally stabilizing.

• Adds support for AA v1.3.r6, which provides users with two new arguments
  • --sv_vcf, --sv_vcf_no_filter/
  • These allow AA to use externally provided SV calls from a VCF file
• Log last_modified date from AA data repo
• Improve usability of --completed_AA_runs mode
• Update github links in container files, documentation, wrapper arguments, and lift singularity scipy version cap
• Bugfixes to GroupedAnalysisAmpSuite.py
• Improve install.sh
• Differentiate various license, report the AA license explicitly since it is not the BSD-2-Clause
• Include copy number flow in cycles_to_bed.py
• Documentation updates

- Python
Published by jluebeck over 2 years ago

ampliconsuite-pipeline - v0.1555.2

• Reallow --ref to be optional if bam file is given
• Require --ref if --completed_AA_runs is given
• Update conda build recipe for local builds
• Bugfix to the default --AA_insert_sdevs argument specified by GroupedAnalysisAmpSuite.py

- Python
Published by jluebeck over 2 years ago

ampliconsuite-pipeline - v0.1555.1

• Updates to GroupedAnalysisAmpSuite.py to add a --no_union option if users want to run multiple samples in a batch but not take union of the seeds.
• add --uninstall option to installer and fix bugs in installer script
• Fix potential issue with concurrent docker/singularity image deployment
• Update conda recipe
• update documentation.
• better logging about issues finding data repo

- Python
Published by jluebeck over 2 years ago

ampliconsuite-pipeline - v0.1546.1

Create a release for packaging with conda.

- Python
Published by jluebeck over 2 years ago