All notable changes to the pipeline-name pipeline.
The format is based on Keep a Changelog.
This project adheres to Semantic Versioning.
- Update README
- Add sanitization to sample IDs to account for standardized filenames
- 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
- Issue with empty email addresses resulting in argument errors
- 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
- Bug with bad params being loaded from default configs
- Bug with call-SRC pipeline getting stuck with DPClust run
- Issue with identifier used in WGS mode
- Call-SRC pipeline
- Input format update to only YAML and to support combinations or BAM/CRAM/FASTQ/SRC inputs
- Issue with status check automatically skipping checks when Slurm commands fail
- Task hash properly handled between WGS and non-WGS modes
- Job submission properly restricted when Slurm query fails
- More descriptive error messages on failure to identify output files
- Add call-sCNA to
requested_pipelines
intemplate.config
- Handling for SRC inputs
- Save nextflow logs sample/patient-specific metapipeline. #187
- 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
- Issue with status check function not properly detecting and reporting pipeline failures
- Issue with pipeline-specific
default.config
overriding parameter settings in metapipeline config
- BAM sample QC pipeline
v1.0.0
- 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
- Recalibrate-BAM no longer runs automatically when not requested
- pipeline-call-sCNA
v3.0.0
and its NFTest - Targeted coverage pipeline
- Option to skip recalibrate-BAM independent of alignment
- 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
- Pipeline ordering option for pipelines downstream of recalibrate-BAM
- Parameter to run pipelines sequentially
- Call-sSNV: 7.0.0-rc.2 -> 8.0.0-rc.1
- Remove validation of pipeline-level parameter from metapipeline level validation
- Default to alt-aware reference for align-DNA
- Re-order FASTQ CSV to match order in align-DNA
- Deletion step for normal BAMs when running multi-sample patients in paired mode
- Make WGS limits dynamically configurable
- Use data structure in params to pass outputs between pipelines
- Update tests
- Update README with current status and parameters
- Update call-sSV
actual
paths innftest.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
- Split call-gSNP into recalibrate-BAM and call-gSNP
- Call-sSNV: 5.0.0 -> 7.0.0-rc.1
- Pass pipeline-specific params through a YAML instead of commandline string
- Call-sSNV outputs no longer overwritten when encountering paired samples in
multi
mode - Allow pipelines to run under job-specific work_dir
- Incorporate user-defined sample-name for "SM" tags when starting from BAM2FASTQ
- Working directory hashes to global limiter job names
- Separate WGS vs non-WGS queues
- Global job volume and submission rate limiter
- 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
- BAM SM tag handling for call-gSNP output filenames
- Empty intervals parameters
- Parameter validation
- Custom schema types with parameter validation
- 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
- Unnecessary
index
field in FASTQ input
- Option for intermediate file saving per pipeline
- align-DNA: 8.1.0 -> 9.0.0
- call-gSNP: 9.2.0 -> 9.2.1
- call-sSV: 4.0.0 -> 5.0.0
- Output tuple emission syntax
- Pipeline selection with FASTQ input
- Pipeline selection options
- Default BAM read group tag values
- Replace tuples with Maps for clarity
- call-gSV v4.0.0
- call-sSV v4.0.0
- Parameterize time interval between job submissions
- call-gSV: 4.0.0 -> 4.0.1
- call-sSNV: 4.0.1 -> 5.0.0
- call-gSNP: 9.1.0 -> 9.2.0
- Support for single-sample mode (single normal and single tumor samples)
- convert-BAM2FASTQ: v2.0.0-rc.1
- Additional call-gSNP params
- Extract submodule version from
nextflow.config
- Identify gSNP
sample_id
based on run mode
- Pipeline selection module
- Option for multi-sample gSNP calling
- Option for multi-sample sSNV Mutect2 calling
- 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
- Use
executor
rate limit to limit job submission rate rather than custom sleep command
- 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
- 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 toignore
- call-mtSNV: 2.0.0 -> 3.0.0-rc.1
- Standardize output directory
site
from inputs
- Remove carriage-return/Windows-specific characters from input examples