Release/0.3.0 by qclayssen · Pull Request #16 · umccr/bolt

qclayssen · 2025-09-15T23:58:59Z

Add

Hypermutation Handling
option for sigrap individual process
--vep_dir required parameter across multiple commands

Upgrade

pcgrr v1.4.1 -> pcgr v2.2.5
gpgr v2.1.3 → v2.2.11
Improve logging

Removed

Removal of COSMIC count and ICGC PCAWG count from rescue logic

* update doc * bump gpgr version

* Bump version: 0.2.15 → 0.2.16 * Change hrd facultative for cancer report (#17) * change hrd file facultatif * fix arg position and assign default value * fix version (#18) * Bump gpgr version to 2.2.0

* Bump version: 0.2.16 → 0.2.17 * bump gpgr to v2.2.1 in docker files (#21)

…11) * add params input for sigrap tools

Copilot

Pull Request Overview

This PR upgrades PCGR from v1.4.1 to v2.2.1 and adds handling for hypermutated samples. The upgrade requires updating field names and annotations to match the new PCGR version's output format, while new functionality filters variants in hypermutated samples to stay within PCGR's variant count limits.

Key changes:

Updated PCGR/CPSR field names to match v2.2.1 output (e.g., PCGR_TIER → PCGR_ACTIONABILITY_TIER)
Added hypermutation handling with variant filtering logic for samples exceeding 450,000 variants
Implemented chunked PCGR processing for large variant sets with parallel execution

Reviewed Changes

Copilot reviewed 19 out of 20 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
pyproject.toml	Version bump to 0.2.17
docker/Dockerfile.pcgr	Updated PCGR conda environment from v1.4.1 to v2.2.1
docker/Dockerfile.gpgr	Updated r-gpgr from 2.1.3 to 2.2.11
conda/env/bolt_env.yml	Added ncurses dependency
bolt/workflows/sv_somatic/annotate.py	Added logging infrastructure
bolt/workflows/smlv_somatic/rescue.py	Added logging infrastructure
bolt/workflows/smlv_somatic/report.py	Added hypermutation variant filtering and updated PCGR integration
bolt/workflows/smlv_somatic/filter.py	Updated field names for PCGR v2.2.1 and added helper function to handle missing values
bolt/workflows/smlv_somatic/annotate.py	Refactored PCGR processing to support chunking and updated field names
bolt/workflows/smlv_germline/report.py	Added logging and vep_dir parameter
bolt/workflows/other/cancer_report.py	Made dragen_hrd_fp optional and added new signature analysis parameters
bolt/util.py	Enhanced command execution with logging, added VCF splitting/merging utilities
bolt/logging_config.py	New logging configuration module
bolt/common/pcgr.py	Major refactor for PCGR v2.2.1 compatibility, chunked processing, and updated field mappings
bolt/common/constants.py	Updated field names and added hypermutation filtering constants
tests/test_smlv_somatic_filter.py	Updated test data to match new PCGR field names
README.md	Updated version references to 0.2.17
CHANGELOG.md	Added changelog entries for recent PRs
.bumpversion.cfg	Updated version to 0.2.17

Comments suppressed due to low confidence (1)

bolt/common/pcgr.py:1

Missing spaces around the == operator. Should be if value == '' or value == '.':

import collections

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bolt/workflows/smlv_somatic/report.py

bolt/workflows/other/cancer_report.py

* update "HIGH_INF_POS" to "HIGH_I_I_POS" in VCF header for latest pcgr version * update constant for pcgr 2.2.5

* change sage vcf header to match 2024 version * move check function * add check in rescue for sage vcf * change for consistencency with pcgr

…arallelisation because OOM hypermutated samples

…'t use more core and so more memory

…e_command. Fixes #26 - Commands now fail immediately instead of continuing silently

Copilot

Pull request overview

Copilot reviewed 20 out of 21 changed files in this pull request and generated 26 comments.

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Copilot · 2026-01-21T03:23:04Z

tests/test_smlv_somatic_filter.py

+    pos='1',
    vid='.',
-    ref='.',
-    alt='.',
+    ref='A',
+    alt='T',


Test data changed from default values to specific values. The change from pos='.' to pos='1', ref='.' to ref='A', and alt='.' to alt='T' looks correct for creating valid test records, but ensure all tests that rely on this function still work correctly with these new default values.

Copilot · 2026-01-21T03:23:04Z

bolt/workflows/smlv_somatic/report.py

+
+        if (variant_count - filter_sum) <= constants.MAX_SOMATIC_VARIANTS:
+            break
+
+        filter_sum += len(variants_sorted.get(key, []))


Logic error in hypermutation filtering: Line 339 checks if (variant_count - filter_sum) <= constants.MAX_SOMATIC_VARIANTS, but filter_sum represents variants to be filtered out, while the condition should check if remaining variants are under the limit. The correct logic should be checking if we've accumulated enough variants to filter to bring the total under the threshold. This could result in incorrect filtering behavior.

Suggested change

if (variant_count - filter_sum) <= constants.MAX_SOMATIC_VARIANTS:

break

filter_sum += len(variants_sorted.get(key, []))

cat_count = len(variants_sorted.get(key, []))

# Check if filtering the variants in this category as well would bring

# the total number of remaining variants under the PCGR limit

if (variant_count - (filter_sum + cat_count)) <= constants.MAX_SOMATIC_VARIANTS:

filter_categories.append(key)

break

filter_sum += cat_count

Copilot · 2026-01-21T03:23:04Z

bolt/workflows/smlv_somatic/annotate.py

+    chunk_size = kwargs.get('pcgr_variant_chunk_size')
+    if chunk_size is not None and chunk_size <= 0:
+        raise click.BadParameter('must be a positive integer', param_hint='--pcgr_variant_chunk_size')
+    chunk_size = chunk_size or constants.MAX_SOMATIC_VARIANTS


Missing validation: Lines 104-105 check if pcgr_variant_chunk_size is negative or zero, but line 106 then allows the value to be None by using chunk_size = chunk_size or constants.MAX_SOMATIC_VARIANTS. However, if a user passes 0, the validation would raise an error. The logic should clarify whether 0 is acceptable (and treated as None) or not. Current implementation is inconsistent.

Suggested change

chunk_size = chunk_size or constants.MAX_SOMATIC_VARIANTS

if chunk_size is None:

chunk_size = constants.MAX_SOMATIC_VARIANTS

bolt/common/constants.py

Copilot · 2026-01-21T03:23:05Z

docker/Dockerfile.pcgr

    --solver libmamba \
    --name pcgr \
-    --file https://raw.githubusercontent.com/sigven/pcgr/v1.4.1/conda/env/lock/pcgr-linux-64.lock
+    --file https://raw.githubusercontent.com/sigven/pcgr/refs/tags/v2.2.5/conda/env/lock/pcgr-linux-64.lock


Version mismatch: The PR description states "pcgrr v1.4.1 -> pcgr v2.2.1", but the Dockerfile is being updated to v2.2.5. The version should be consistent with what's documented in the PR description or the description should be updated to reflect v2.2.5.

Copilot · 2026-01-21T03:23:09Z

bolt/workflows/smlv_somatic/report.py

+
+    # Set filter category for each variant
+    variants_sorted = collections.defaultdict(list)
+    for variant_count, variant in enumerate(cyvcf2.VCF(fp_annotated_out), 1):


Variable naming issue: Line 321 uses for variant_count, variant in enumerate(cyvcf2.VCF(fp_annotated_out), 1), which shadows the outer scope where variant_count might be used later (line 339). This can lead to confusion. Consider using a different variable name like idx or i for the enumeration.

bolt/workflows/other/cancer_report.py

Copilot · 2026-01-21T03:23:09Z

bolt/workflows/other/cancer_report.py



 import click
+import logging


Import of 'logging' is not used.

bolt/common/pcgr.py

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Copilot

Pull request overview

Copilot reviewed 20 out of 21 changed files in this pull request and generated 11 comments.

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Copilot · 2026-02-19T04:56:04Z

docker/Dockerfile.pcgr

  conda create \
    --solver libmamba \
    --name pcgr \
-    --file https://raw.githubusercontent.com/sigven/pcgr/v1.4.1/conda/env/lock/pcgr-linux-64.lock
+    --file https://raw.githubusercontent.com/sigven/pcgr/refs/tags/v2.2.5/conda/env/lock/pcgr-linux-64.lock

 RUN \
  conda create \
    --solver libmamba \
    --name pcgrr \
-    --file https://raw.githubusercontent.com/sigven/pcgr/v1.4.1/conda/env/lock/pcgrr-linux-64.lock
+    --file https://raw.githubusercontent.com/sigven/pcgr/refs/tags/v2.2.5/conda/env/lock/pcgrr-linux-64.lock


The PR description says PCGR is upgraded to v2.2.1, but this Dockerfile pulls lock files from tag v2.2.5. Either update the PR description/release notes to match, or change the Dockerfile to the intended PCGR version so the built image matches what’s documented.

Copilot · 2026-02-19T04:56:04Z

README.md

 | Name    | Docker image URI                    | Commands                       |
 | ---     | ---                                 | ---                            |
-| pcgr    | ghcr.io/scwatts/bolt:0.2.14-pcgr    | • `bolt smlv_germline report`<br />• `bolt smlv_somatic annotate`<br />• `bolt smlv_somatic report`<br /> |
-| gpgr    | ghcr.io/scwatts/bolt:0.2.14-gpgr    | • `bolt other cancer_report`   |
-| snpeff  | ghcr.io/scwatts/bolt:0.2.14-snpeff  | • `bolt sv_somatic annotate`   |
-| circos  | ghcr.io/scwatts/bolt:0.2.14-circos  | • `bolt other purple_baf_plot` |
-| multiqc | ghcr.io/scwatts/bolt:0.2.14-multiqc | • `bolt other multiqc_report`  |
-| base    | ghcr.io/scwatts/bolt:0.2.14         | • `bolt smlv_germline prepare`<br />• `bolt smlv_somatic rescue`<br />• `bolt smlv_somatic filter`<br />• `bolt sv_somatic prioritise`<br /> |
+| pcgr    | ghcr.io/scwatts/bolt:0.2.17-pcgr    | • `bolt smlv_germline report`<br />• `bolt smlv_somatic annotate`<br />• `bolt smlv_somatic report`<br /> |
+| gpgr    | ghcr.io/scwatts/bolt:0.2.17-gpgr    | • `bolt other cancer_report`   |
+| snpeff  | ghcr.io/scwatts/bolt:0.2.17-snpeff  | • `bolt sv_somatic annotate`   |
+| circos  | ghcr.io/scwatts/bolt:0.2.17-circos  | • `bolt other purple_baf_plot` |
+| multiqc | ghcr.io/scwatts/bolt:0.2.17-multiqc | • `bolt other multiqc_report`  |
+| base    | ghcr.io/scwatts/bolt:0.2.17         | • `bolt smlv_germline prepare`<br />• `bolt smlv_somatic rescue`<br />• `bolt smlv_somatic filter`<br />• `bolt sv_somatic prioritise`<br /> |

 ## Usage

 Given the nature of software dependencies required, it is strongly recommended to run `bolt` commands via the existing
 [Docker images](#docker-images):

 ```bash
-docker run -ti -v $(pwd):$(pwd) -w $(pwd) ghcr.io/scwatts/bolt:0.2.14 \
+docker run -ti -v $(pwd):$(pwd) -w $(pwd) ghcr.io/scwatts/bolt:0.2.17 \
  bolt smlv_somatic filter \


README Docker image tags are set to 0.2.17, but the project version in pyproject.toml/.bumpversion.cfg is 0.3.0. Update the README image URIs and example docker run command to reference the same release version to avoid publishing/usage confusion.

Copilot · 2026-02-19T04:56:04Z

CHANGELOG.md

 - [3](https://github.com/scwatts/bolt/pull/3) - Improve PCGR / CPSR argument handling

- [6](https://github.com/umccr/bolt/pull/6) - Change oncoanalyser v2.0.0 uptade, with switch sv caller from GRIPSS to eSVee
+- [6](https://github.com/umccr/bolt/pull/6) - Change oncoanalyser v2.0.0 uptade, with switch sv caller from GRIPSS to eSVee


Typo in changelog entry: "uptade" should be "update".

Suggested change

- [6](https://github.com/umccr/bolt/pull/6) - Change oncoanalyser v2.0.0 uptade, with switch sv caller from GRIPSS to eSVee

- [6](https://github.com/umccr/bolt/pull/6) - Change oncoanalyser v2.0.0 update, with switch sv caller from GRIPSS to eSVee

Copilot · 2026-02-19T04:56:04Z

bolt/workflows/smlv_somatic/report.py

+        filter_category = (data['tier'], *variant_filter)
+        variant_repr = pcgr.get_variant_repr(variant)
+        variants_sorted[filter_category].append(variant_repr)


filter_category prefixes with data['tier'] from PCGR_ACTIONABILITY_TIER (values like '1'..'4'/'N'), but pcgr.get_ordering() iterates tiers from constants.PCGR_TIERS_FILTERING (currently TIER_1…/NONCODING). With this mismatch, variants_sorted.get(key, []) won’t match and hypermutation down-selection won’t actually reduce the VCF below MAX_SOMATIC_VARIANTS. Align tier values (constants and/or mapping) so ordering keys match data['tier'].

Copilot · 2026-02-19T04:56:05Z

bolt/workflows/smlv_somatic/annotate.py

    #       - PCGR ACMG TIER [INFO/PCGR_TIER]
    #       - VEP consequence [INFO/PCR_CSQ]
    #       - Known mutation hotspot [INFO/PCGR_MUTATION_HOTSPOT]
-    #       - ClinVar clinical significant [INFO/PCGR_CLINVAR_CLNSIG]
-    #       - Hits in COSMIC [INFO/PCGR_COSMIC_COUNT]
+    #       - ClinVar clinical significant [INFO/PCGR_CLNSIG]
    #       - Hits in TCGA [INFO/PCGR_TCGA_PANCANCER_COUNT]


These comments still reference legacy PCGR output fields (PCGR_TIER, PCGR_CLINVAR_CLNSIG, COSMIC/PCAWG counts), but the code/constants have moved to PCGR_ACTIONABILITY_TIER and PCGR_CLINVAR_CLASSIFICATION and no longer transfer COSMIC/PCAWG counts. Update the comment block to match the current annotations being transferred.

Copilot · 2026-02-19T04:56:05Z

bolt/common/constants.py

+PCGR_TIERS_FILTERING = (
    'TIER_1',
    'TIER_2',
-}
+    'TIER_3',
+    'TIER_4',
+    'NONCODING',
+)


PCGR_TIERS_FILTERING is defined as TIER_1…NONCODING, but the code normalizes/uses actionability tiers as '1'..'4' / 'N' (see bolt/common/pcgr.py where PCGR_ACTIONABILITY_TIER is set). This mismatch breaks tier-based ordering/filtering (e.g., hypermutation down-selection). Align the constants with the actual tier values used in VCF/TSV, or add a mapping layer.

Copilot · 2026-02-19T04:56:05Z

bolt/workflows/smlv_somatic/report.py

+    ''')
+
+    # Set filter category for each variant
+    variants_sorted = collections.defaultdict(list)


variant_count is introduced by the enumerate(..., 1) loop, but it’s later used after the loop to decide whether enough variants have been filtered out. If the annotated VCF has zero records, variant_count will be undefined and raise UnboundLocalError. Initialize variant_count = 0 before the loop (or compute total count explicitly).

Suggested change

variants_sorted = collections.defaultdict(list)

variants_sorted = collections.defaultdict(list)

variant_count = 0

bolt/common/pcgr.py

bolt/util.py

Copilot · 2026-02-19T04:56:06Z

docker/Dockerfile.pcgr

+    --file https://raw.githubusercontent.com/sigven/pcgr/refs/tags/v2.2.5/conda/env/lock/pcgr-linux-64.lock

 RUN \
  conda create \
    --solver libmamba \
    --name pcgrr \
-    --file https://raw.githubusercontent.com/sigven/pcgr/v1.4.1/conda/env/lock/pcgrr-linux-64.lock
+    --file https://raw.githubusercontent.com/sigven/pcgr/refs/tags/v2.2.5/conda/env/lock/pcgrr-linux-64.lock


The Docker build downloads conda lockfiles for pcgr and pcgrr directly from raw.githubusercontent.com using only a tag reference, which can change over time. If the upstream repository or tag is compromised, an attacker could modify the environment definition to pull and execute malicious packages during image build or when the container runs, leading to a supply-chain compromise. To reduce this risk, pin these URLs to immutable commit SHAs or vendor the lockfiles into this repository and verify their integrity before use.

Release v0.2.15 (#14)

b59abbe

* update doc * bump gpgr version

qclayssen self-assigned this Sep 15, 2025

qclayssen and others added 9 commits September 23, 2025 17:00

fix version (#18)

f3696db

Bump gpgr version to 2.2.0

a4bfad1

Release 0.2.16 (#19)

05c1fa2

* Bump version: 0.2.15 → 0.2.16 * Change hrd facultative for cancer report (#17) * change hrd file facultatif * fix arg position and assign default value * fix version (#18) * Bump gpgr version to 2.2.0

Release 0.2.17 (#20)

6dd0b09

* Bump version: 0.2.16 → 0.2.17 * bump gpgr to v2.2.1 in docker files (#21)

Add option for sash sigrap individual process input to cancer report (#…

d7ca46b

…11) * add params input for sigrap tools

Hypermutation Handling in PCGR (#9)

f33c48c

Feature/pcgr v2.2.1 (#10)

cb5ee4d

fix merge duplication and imports

9d8e4d1

bump pcgr version

8db35b3

qclayssen force-pushed the release/0.3.0 branch from ec2700b to 8db35b3 Compare October 2, 2025 04:18

qclayssen added 3 commits October 2, 2025 14:19

bump gpgr version

c67b30a

change print to logging

f9a7d3b

add argument chunck size

b8ee4a0

qclayssen force-pushed the release/0.3.0 branch 2 times, most recently from 54672c1 to 9c613d4 Compare October 17, 2025 00:38

fix version software pcgr container

8223ef9

qclayssen force-pushed the release/0.3.0 branch from 9c613d4 to 8223ef9 Compare October 17, 2025 00:44

qclayssen added 5 commits October 17, 2025 15:50

add logging and filter fonction to read value and replace placeholder

f83c23a

fix indentation

22b5c12

read gz tsv from pcgr

529309c

change PCGR_CLINVAR_CLASSIFICATION

d3dd182

Change pcgr header check

a5fc923

qclayssen requested a review from Copilot October 24, 2025 00:46

Copilot AI reviewed Oct 24, 2025

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qclayssen added 3 commits October 24, 2025 13:56

tyo

bf930e7

typo

8ea1edc

add missing variable pcgr_output_dir

443c5be

qclayssen mentioned this pull request Nov 11, 2025

Uptade sage vcf header check #24

Merged

qclayssen and others added 7 commits November 19, 2025 14:25

Pcgr v2.2.5 (#22)

966967f

* update "HIGH_INF_POS" to "HIGH_I_I_POS" in VCF header for latest pcgr version * update constant for pcgr 2.2.5

Uptade sage vcf header check (#24)

6a93f6b

* change sage vcf header to match 2024 version * move check function * add check in rescue for sage vcf * change for consistencency with pcgr

add missing HMF_HOTSPOT constant

ed3b11b

Fix quotation

a3d16f7

Fix test

9ddeac8

remove PCGR html report from chunk (hypermutated) to reduce memory use

41b83bb

change remove pcgr parallelisation of chunks, and fix pcgr internal p…

c42d725

…arallelisation because OOM hypermutated samples

qclayssen force-pushed the release/0.3.0 branch from 24be1fb to c42d725 Compare December 17, 2025 04:25

free disk worker

03bba1d

qclayssen force-pushed the release/0.3.0 branch from a4beb4d to 03bba1d Compare December 17, 2025 05:00

qclayssen added 4 commits December 19, 2025 14:56

remove exception to stop at fail process

cb1c39b

make thread you by pcgr constant, so in case of OOM, on the retry don…

27403cb

…'t use more core and so more memory

Fix silent command failures by integrating error handling into execut…

2902428

…e_command. Fixes #26 - Commands now fail immediately instead of continuing silently

Extract PCGR errors from log files

15db538

qclayssen mentioned this pull request Jan 21, 2026

Release/0.7.0 umccr/sash#39

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qclayssen requested a review from Copilot January 21, 2026 03:16

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qclayssen and others added 2 commits January 21, 2026 14:32

Update bolt/workflows/other/cancer_report.py

9bf22f5

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Update bolt/common/pcgr.py

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Apply suggestions from code review

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qclayssen added 4 commits February 19, 2026 16:06

fix typo

dbd500f

remove duplicate fonction

3d2d7b1

fix typo

15f0247

add check pcgr_hotspot_present value

8fa85ef

-        if (variant_count - filter_sum) <= constants.MAX_SOMATIC_VARIANTS:
-            break
-        filter_sum += len(variants_sorted.get(key, []))
+        cat_count = len(variants_sorted.get(key, []))
+        # Check if filtering the variants in this category as well would bring
+        # the total number of remaining variants under the PCGR limit
+        if (variant_count - (filter_sum + cat_count)) <= constants.MAX_SOMATIC_VARIANTS:
+            filter_categories.append(key)
+            break
+        filter_sum += cat_count

	chunk_size = chunk_size or constants.MAX_SOMATIC_VARIANTS
	if chunk_size is None:
	chunk_size = constants.MAX_SOMATIC_VARIANTS

	- [6](https://github.com/umccr/bolt/pull/6) - Change oncoanalyser v2.0.0 uptade, with switch sv caller from GRIPSS to eSVee
	- [6](https://github.com/umccr/bolt/pull/6) - Change oncoanalyser v2.0.0 update, with switch sv caller from GRIPSS to eSVee

	variants_sorted = collections.defaultdict(list)
	variants_sorted = collections.defaultdict(list)
	variant_count = 0

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qclayssen commented Sep 15, 2025 •

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