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CHANGELOG.md

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Changelog

All notable changes to the pipeline-name pipeline.

The format is based on Keep a Changelog.

This project adheres to Semantic Versioning.

[Unreleased]

Changed

  • Update README
  • Add sanitization to sample IDs to account for standardized filenames

[6.0.0] - 2024-07-10

Changed

  • Call-SRC: 2.0.0-rc.1 -> 2.0.0
  • Align-DNA: 10.0.0 -> 10.1.0
  • Recalibrate-BAM: 1.0.0 -> 1.0.1
  • Call-sSNV: 8.0.0 -> 8.1.0
  • Call-gSV: 5.0.0 -> 5.2.0
  • Call-sCNA: 3.1.0 -> 3.2.0

Fixed

  • Issue with empty email addresses resulting in argument errors

[6.0.0-rc.6] - 2024-06-12

Added

  • Support for inputs to be given through a CSV
  • Nextflow wrapper script to capture and consolidate all pipeline logs for a sample
  • status_email_address parameter to send started/completed emails for child pipelines

Fixed

  • Bug with bad params being loaded from default configs
  • Bug with call-SRC pipeline getting stuck with DPClust run

[6.0.0-rc.5] - 2024-05-29

Fixed

  • Issue with identifier used in WGS mode

[6.0.0-rc.5] - 2024-05-23 - YANKED

Added

  • Call-SRC pipeline

Changed

  • Input format update to only YAML and to support combinations or BAM/CRAM/FASTQ/SRC inputs

Fixed

  • Issue with status check automatically skipping checks when Slurm commands fail

[6.0.0-rc.4] - 2024-05-15

Fixed

  • Task hash properly handled between WGS and non-WGS modes
  • Job submission properly restricted when Slurm query fails

[6.0.0-rc.3] - 2024-05-13

Added

  • More descriptive error messages on failure to identify output files
  • Add call-sCNA to requested_pipelines in template.config
  • Handling for SRC inputs
  • Save nextflow logs sample/patient-specific metapipeline. #187

Changed

  • Use GitHub container registry CI/CD check
  • Calculate-targeted-coverage: 1.0.0-rc.2 -> 1.1.0
  • Call-gSNP: 10.0.0 -> 10.0.1
  • Align-DNA: 10.0.0-rc.1 -> 10.0.0
  • Call-mtSNV: 4.0.0-rc.1 -> 4.0.0
  • Call-gSV: 5.0.0-rc.1 -> 5.0.0
  • Call-sCNA: 3.0.0 -> 3.1.0
  • Require parameters only for pipelines being run
  • Validate parameters only for pipelines being run

Fixed

  • Issue with status check function not properly detecting and reporting pipeline failures
  • Issue with pipeline-specific default.config overriding parameter settings in metapipeline config

[6.0.0-rc.2] - 2024-03-22

Added

  • BAM sample QC pipeline v1.0.0

Changed

  • Call-sSNV: 8.0.0-rc.1 -> 8.0.0
  • Call-gSNP: 10.0.0-rc.3 -> 10.0.0
  • Call-mtSNV: 3.0.0 -> 4.0.0-rc.1
  • Call-gSV: 4.0.1 -> 5.0.0-rc.1
  • Recalibrate-BAM: 1.0.0-rc.4 -> 1.0.0
  • call-sSV: 6.0.0-rc.1 -> 6.1.0
  • Allow downstream pipelines to fail gracefully without affecting failure of other pipelines
  • Allow waiting on multiple dependencies per pipeline before submission

Fixed

  • Recalibrate-BAM no longer runs automatically when not requested

[6.0.0-rc.1] - 2024-03-11

Added

  • pipeline-call-sCNA v3.0.0 and its NFTest
  • Targeted coverage pipeline
  • Option to skip recalibrate-BAM independent of alignment

Changed

  • Convert-BAM2FASTQ: 2.0.0-rc.1 -> 2.0.0-rc.2
  • Align-DNA: 9.0.0 -> 10.0.0-rc.1
  • Sanitize metadata passed to align-DNA
  • Calculate-targeted-coverage: update name from targeted-coverage
  • Save logs and input files for all pipelines
  • Update test samples

[5.3.1] - 2024-01-10

Added

  • Pipeline ordering option for pipelines downstream of recalibrate-BAM
  • Parameter to run pipelines sequentially

Changed

  • Call-sSNV: 7.0.0-rc.2 -> 8.0.0-rc.1

[5.2.1] - 2023-12-07

Removed

  • Remove validation of pipeline-level parameter from metapipeline level validation

[5.2.0] - 2023-11-17

Changed

  • Default to alt-aware reference for align-DNA
  • Re-order FASTQ CSV to match order in align-DNA

Added

  • Deletion step for normal BAMs when running multi-sample patients in paired mode

[5.1.0] - 2023-10-30

Changed

  • Make WGS limits dynamically configurable

[5.0.0] - 2023-10-25

Changed

  • Use data structure in params to pass outputs between pipelines
  • Update tests
  • Update README with current status and parameters

[5.0.0-rc.10] - 2023-10-10

Changed

  • Update call-sSV actual paths in nftest.yaml
  • Update input structure for call-sSV 6.0.0-rc.1
  • Update call-sSV 6.0.0-rc.1
  • Update tests to conform to pipeline and nftest updates.
  • Call-sSNV: 5.0.0 -> 7.0.0-rc.2

[5.0.0-rc.9] - 2023-08-24

Changed

  • Split call-gSNP into recalibrate-BAM and call-gSNP
  • Call-sSNV: 5.0.0 -> 7.0.0-rc.1

[5.0.0-rc.8] - 2023-08-11

Changed

  • Pass pipeline-specific params through a YAML instead of commandline string

Fixed

  • Call-sSNV outputs no longer overwritten when encountering paired samples in multi mode
  • Allow pipelines to run under job-specific work_dir

[5.0.0-rc.7] - 2023-08-03

Added

  • Incorporate user-defined sample-name for "SM" tags when starting from BAM2FASTQ

[5.0.0-rc.6] - 2023-07-13

Added

  • Working directory hashes to global limiter job names
  • Separate WGS vs non-WGS queues

[5.0.0-rc.5] - 2023-06-16

Added

  • Global job volume and submission rate limiter

Changed

  • Handle pipeline-specific params without a hard-coded list per pipeline
  • Update tests for current pipeline versions
  • Update handling of output_dir param to avoid modifications

Fixed

  • BAM SM tag handling for call-gSNP output filenames
  • Empty intervals parameters

[5.0.0-rc.4] - 2023-05-04

Added

  • Parameter validation
  • Custom schema types with parameter validation

Changed

  • Standardize process and script names
  • Automatically detect CPU and memory for specified partition type
  • Automate setting of subworkflow CPUs
  • Divide /scratch into pipeline-specific directories for deletion once pipeline ends
  • Slurm job name to include work directory path

Removed

  • Unnecessary index field in FASTQ input

[5.0.0-rc.3] - 2023-02-08

Added

  • Option for intermediate file saving per pipeline

[5.0.0-rc.2] - 2023-02-06

Changed

  • align-DNA: 8.1.0 -> 9.0.0
  • call-gSNP: 9.2.0 -> 9.2.1
  • call-sSV: 4.0.0 -> 5.0.0

Fixed

  • Output tuple emission syntax
  • Pipeline selection with FASTQ input

[5.0.0-rc.1] - 2023-01-30

Added

  • Pipeline selection options
  • Default BAM read group tag values

Changed

  • Replace tuples with Maps for clarity

[4.0.0] - 2022-12-19

Added

  • call-gSV v4.0.0
  • call-sSV v4.0.0

Changed

  • Parameterize time interval between job submissions
  • call-gSV: 4.0.0 -> 4.0.1

[3.0.0] - 2022-11-23

Changed

  • call-sSNV: 4.0.1 -> 5.0.0
  • call-gSNP: 9.1.0 -> 9.2.0

[3.0.0-rc.1] - 2022-11-08

Added

  • Support for single-sample mode (single normal and single tumor samples)

Changed

  • convert-BAM2FASTQ: v2.0.0-rc.1

[2.0.0] - 2022-10-13

Added

  • Additional call-gSNP params

Changed

  • Extract submodule version from nextflow.config
  • Identify gSNP sample_id based on run mode

[2.0.0-rc.1] - 2022-09-30

Added

  • Pipeline selection module
  • Option for multi-sample gSNP calling
  • Option for multi-sample sSNV Mutect2 calling

Changed

  • Merge configs into one config
  • call-mtSNV: 3.0.0-rc.1 -> 3.0.0
  • call-gSNP: 9.0.1 -> 9.1.0
  • align-DNA: 8.0.0 -> 8.1.0
  • Standardize directories to use singular form

[1.0.0] - 2022-07-29

Changed

  • Use executor rate limit to limit job submission rate rather than custom sleep command

[1.0.0-rc.1] - 2022-07-15

Added

  • Main pipelines, including convert-BAM2FASTQ, align-DNA, call-gSNP, call-sSNV, and call-mtSNV.
  • "Unit tests" with a downsampled CPTAC WGS sample.
  • Nextflow testing module
  • Checks for working directories
  • YAML input
  • GPL2 license

Changed

  • Standardize output directory
  • Reduce number of temp files in /hot
  • align-DNA: 7.3.1 -> 8.0.0
  • call-gSNP: 7.2.1 -> 9.0.1
  • call-sSNV: 3.0.0-rc.1 -> 4.0.1
  • Automatically set the work_dir parameter for ucla_cds
  • Update README
  • Main process errorStrategy set to ignore
  • call-mtSNV: 2.0.0 -> 3.0.0-rc.1
  • Standardize output directory

Removed

  • site from inputs

Fixed

  • Remove carriage-return/Windows-specific characters from input examples