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RENEE development version

  • Fix ResourceWarning: unclosed <socket> from PySimpleGUI being imported at module level. (#276, @kelly-sovacool, @copilot)

RENEE 2.7.5

  • Added more memory to rule validator. (#263, @samarth8392)
  • New --time option for renee run and renee build to override the default SLURM walltime. (#269, @kelly-sovacool)
    • Also fix bug where --partition was not being propagated to the sbatch call.
  • Documentation improvements: fix the jobby output filename and formatting problems. (#274, @kelly-sovacool)

RENEE 2.7.4

  • New --partition option for renee run and renee build to specify the SLURM partition. (#252, @kelly-sovacool)
    • This feature is necessary for users who do not have access to the norm partition on biowulf, such as students.
  • Fix bug in phred_encoding.py that incorrectly detected Phred+33 files as Phred+64, causing BBMerge to fail. (#257, @kelly-sovacool)

RENEE 2.7.3

  • Bug fixes: (#246, @kelly-sovacool)
    • Increase memory for fastq screen.
    • Do not proceed to trimming if fastq validator fails.
    • Fix typo in docs.

RENEE 2.7.2

  • Fix typos in documentation. (#240, @Ramlah7)
  • Fix bug in renee build that caused dry run & run to fail with a syntax error. (#244, @kelly-sovacool)

RENEE 2.7.1

  • Improvements for fastq validator: (#224, @kelly-sovacool)
    • Increase default memory.
    • Capture stdout in a log file so the output is not deleted on failure.
  • Fix broken symlinks for genome reference files on biowulf. (#226, @kelly-sovacool)

RENEE 2.7.0

  • RENEE now depends on ccbr_tools v0.4 for updated jobby & spooker utilities. (#207, @kelly-sovacool)
  • Add mmul10_108 (rhesus macaque) to list of reference genomes. (#212, @kelly-sovacool)
  • Added support for new reference genomes on biowulf:
    • mm39_M36 (#199, @kelly-sovacool)
    • mm39_M37 (#220, @kelly-sovacool)
    • hg38_48 (#220, @kelly-sovacool)
  • Fix --sif-cache example in docs. (#208, @kelly-sovacool)

RENEE 2.6.8

  • Fix broken symlinks for genome reference files on biowulf. (#226, @kelly-sovacool)

RENEE 2.6.7

  • Minor CLI fixes. (#202, #203, @kelly-sovacool)

RENEE 2.6.6

  • Minor documentation updates. (#198, @kelly-sovacool)

RENEE 2.6.5

  • Critical bug fix: use local copies of Arriba resources for biowulf & frce instead of downloading them from an S3 bucket. (#191, @kelly-sovacool)
  • Increase memory for fastq_screen. (#188, @kelly-sovacool)

RENEE 2.6.4

  • Fix spelling of shared SIF directory on biowulf -- it is /data/CCBR_Pipeliner/SIFs with a lowercase "s" at the end. (#182, @kelly-sovacool)
  • Raise an error if too few reads are left after trimming with cutadapt. (#184, @kelly-sovacool)
  • Reformat GTF files during renee build that are missing 'gene_biotype' or 'gene_type' attributes in exons. (#185, @kelly-sovacool)
  • Add support for the marmoset genome (mCalJac1 2021). (#185, @kelly-sovacool)

RENEE 2.6.3

  • Upgrade containers to fix $PYTHONPATH clashes in fc_lane, inner_distance, tin, tin_merge, and rnaseq_multiqc. (#176, @kelly-sovacool)
  • Fix error that prevented existing output directories from being re-run. (#176, @kelly-sovacool)
  • Fix error in renee build where image_cache() wasn't imported. (#178, @kelly-sovacool)

RENEE 2.6.2

  • Consolidate build_cluster.json into cluster.json. (#167, @kelly-sovacool)
  • Remove unused miniconda container. (#168, @kelly-sovacool)
  • Fix error in RSEQC rules. (#172, @kelly-sovacool)

RENEE 2.6.1

  • New contributing guide available on GitHub and the documentation website. (#159, @kelly-sovacool)
  • New renee debug subcommand to determine the base directory for debugging purposes. (#159, @kelly-sovacool)
  • Fix renee cache subcommand to correctly read the container images config file. (#163, @kelly-sovacool)

RENEE 2.6.0

New features

  • Support hg38 release 45 on biowulf & FRCE. (#127, @kelly-sovacool)
  • hg38 genome index files now include decoy & virus sequences. (#136, @kelly-sovacool)
    • Additionally, --genome is no longer required and is set to hg38_36 by default.
  • Set default shared singularity SIF directory for biowulf and frce. (#94, @kelly-sovacool)
  • Add renee gui subcommand to launch the graphical user interface. (#94, @kelly-sovacool)
    • Previously, renee_gui (with an underscore) was a command in the ccbrpipeliner module.

Bug fixes

  • Ensure renee build creates necessary config directory during initialization. (#139, @kelly-sovacool)
  • Run rsem-generate-data-matrix to create gene and isoform matrix files. (#149, @kelly-sovacool)
  • Fix bug in the driver script that caused the snakemake module not to be loaded on biowulf in some cases. (#154, @kelly-sovacool)

Documentation updates

  • Minor documentation improvements. (#132, #135, #152, @kelly-sovacool)
  • Add GUI instructions to the documentation website. (#38, @samarth8392)
  • The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#150, @kelly-sovacool)
  • Show the name of the pipeline rather than the python script for CLI help messages. (#131, @kelly-sovacool)
  • Added Expected output tab to the documentation website and updated FAQs (#156, @samarth8392)

RENEE 2.5.13

  • Backport all genome config files from v2.6.5. (#196, @kelly-sovacool)
    • Critical bug fix due to missing S3 bucket. (#191)
    • Rebuild hg19 & hg38 references from GDC. (#136)
    • Add marmoset genome. (#185)

RENEE 2.5.12

  • Minor documentation improvements. (#100, @kelly-sovacool)
  • Fix RNA report bug, caused by hard-coding of PC1-3, when only PC1-2 were generated. (#104, @slsevilla)
  • Allow printing the version or help message even if singularity is not in the path. (#110, @kelly-sovacool)
  • Fix RSeQC environments:
    • Set RSeQC envmodule version to 4.0.0, which synchronizes it with the version in the docker container used by singularity. (#122, @kelly-sovacool)
    • Update docker with RSeQC's tools properly added to the path. (#123, @kelly-sovacool)

RENEE 2.5.11

  • Create a citation file to describe how to cite RENEE. (#86, @kelly-sovacool)
  • Set HPC-specific fastq screen config and kraken DB paths for Biowulf and FRCE. (#78, @kelly-sovacool)
    • Previously, FRCE users were required to set --shared-resources, which were kept in a location on FRCE not under version control. This change brings the paths under version control so they're easier to recover if deleted.
  • Fix permissions to allow read/write access to the scripts dir which caused rNA report to fail (#91, @slsevilla)
  • Fix RSEM reference and rRNA interval list paths in FRCE-specific config files (#85, @kelly-sovacool & @slsevilla)
  • Fix bug which caused incorrect genome annotation JSON files to be used (#87, @kelly-sovacool)
  • Set default temporary directory depending on HPC platform. (#98, @kelly-sovacool)

RENEE 2.5.10

  • Fix a bug that caused slurm jobs to fail. (#74, @kopardev)

RENEE 2.5.9

  • Fix bugs that prevented single-end data from running through the pipeline. (#58, @kelly-sovacool)
  • Increase wall time for kraken and bbmerge rules. (#68, @slsevilla)

RENEE 2.5

  • SLURM_SUBMIT_HOST adding to get hostname correctly on compute nodes.
  • config.json is only created when runmode==init and is no longer recreated or overwritten when runmode==run or when resuming a previously unsuccessful run.
  • prebuilt*list, a list of <genome>*<gencode_annotation> combos is auto-populated by glob-ing for relevant JSON files in the RENEEDIR/resources folder.

RENEE 2.4

  • "pipelinehome" added to config.json in output folder.
  • cluster.json optimized.
  • "\.R1$", "\.R2$" added to workflow/scripts/pyparser.py. This helps FQscreen2 output correctly collected in the multiqc_matrix.tsv which is required for rNA report HTML.

RENEE 2.3

  • runner orchestration script updated for:
    • --wait and --create-nidap-folder options added for frce. Also work on biowulf. These are required when running RENEE with NIDAP API call.
    • --rerun-triggers mtime set when snakemake version is >= 7.8
  • spooker updated to track user info on frce.
  • NIDAP folder related updates made to Snakefile. rules/nidap.smk added.
  • "_2" suffix added to "FQscreen2" files to distinguish them from "FQscreen" files. Now two separate fqscreen plots per sample are reported in the multiqc report.
  • Custom Kraken2 database created and used. The "Standard" Kraken2 database was missing mouse genome.. hence it was added.

RENEE v2.2

  • spooker utility added to onsuccess and onerror blocks in Snakefile. Only works for biowulf.

RENEE 2.1

  • spooker utility added to track userdata on biowulf.
  • CLI support for frce implemented.
  • resource jsons split into 2 folders biowulf and frce to store HPC-specific JSONs.
  • resource bundles created on both, biowulf and frce, for 4 hg38 and 3 mm10 genome+annotation combinations.

RENEE 2.0

  • new name RENEE
  • redirect wrapper script added.
  • MultiQC version changed from v1.9 to v1.12. resources/multiqc_config.yaml updated accordingly.
  • updates to project.json and tools.json templates.
  • updates to builder, cacher and runner workflow orchestration scripts.
  • resources/gff3togtf.py, resources/jobby and resources/run_jobby_on_snakemake_log added.
  • adding jobby related commands to onsuccess and onerror blocks in Snakefile.
  • fastQValidator: -minReadLen 2 added to command line.
  • GTF now parsed at STAR command line. GTF-agnostic STAR index can be reused saving significant disk space in the "resources" folder.