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Pcgr v2.2.5 #22

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90feada
Add option for sash sigrap individual process input to cancer report …
qclayssen Aug 27, 2025
8780e2f
Hypermutation Handling in PCGR (#9)
qclayssen Aug 29, 2025
f84fbcd
Feature/pcgr v2.2.1 (#10)
qclayssen Sep 2, 2025
53fa6e8
fix merge duplication and imports
qclayssen Sep 16, 2025
c26368a
update container
qclayssen Sep 25, 2025
ea5cdf4
add login
qclayssen Sep 30, 2025
389a79b
bump gpgr version
qclayssen Oct 2, 2025
a084ad4
update "HIGH_INF_POS" to "HIGH_I_I_POS" in VCF header for latest pcgr…
qclayssen Oct 3, 2025
9280dc0
Merge branch 'release/0.3.0' into pcgr-v2.2.5
qclayssen Oct 22, 2025
0fb4479
update constant for pcgr 2.2.5
qclayssen Oct 23, 2025
aefedc5
fix typo
qclayssen Oct 23, 2025
9013224
Apply suggestion from @Copilot
qclayssen Oct 24, 2025
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17 changes: 5 additions & 12 deletions bolt/common/constants.py
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Original file line number Diff line number Diff line change
Expand Up @@ -288,8 +288,10 @@ def namespace(self):
'MANE|MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|'
'UNIPROT_ISOFORM|RefSeq|DOMAINS|HGVS_OFFSET|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|'
'gnomADe_ASJ_AF|gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|'
'gnomADe_REMAINING_AF|gnomADe_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|'
'MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|'
'gnomADe_REMAINING_AF|gnomADe_SAS_AF|gnomADg_AF|gnomADg_AFR_AF|gnomADg_AMI_AF|'
'gnomADg_AMR_AF|gnomADg_ASJ_AF|gnomADg_EAS_AF|gnomADg_FIN_AF|gnomADg_MID_AF|'
'gnomADg_NFE_AF|gnomADg_REMAINING_AF|gnomADg_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|'
'MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|'
'MaxEntScan_alt|MaxEntScan_diff|MaxEntScan_ref'
),
},
Expand Down Expand Up @@ -328,16 +330,7 @@ def namespace(self):
'Number': '.',
'Type': 'String',
'Description': (
'Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|'
'Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|'
'Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|'
'FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE|MANE_SELECT|'
'MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|'
'DOMAINS|HGVS_OFFSET|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|gnomADe_ASJ_AF|'
'gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|gnomADe_REMAINING_AF|'
'gnomADe_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|'
'MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|MaxEntScan_alt|MaxEntScan_diff|'
'MaxEntScan_ref'
'Consequence annotations from Ensembl VEP. Format: Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|ALLELE_NUM|DISTANCE|STRAND|FLAGS|PICK|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|MANE|MANE_SELECT|MANE_PLUS_CLINICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|UNIPROT_ISOFORM|RefSeq|DOMAINS|HGVS_OFFSET|gnomADe_AF|gnomADe_AFR_AF|gnomADe_AMR_AF|gnomADe_ASJ_AF|gnomADe_EAS_AF|gnomADe_FIN_AF|gnomADe_MID_AF|gnomADe_NFE_AF|gnomADe_REMAINING_AF|gnomADe_SAS_AF|gnomADg_AF|gnomADg_AFR_AF|gnomADg_AMI_AF|gnomADg_AMR_AF|gnomADg_ASJ_AF|gnomADg_EAS_AF|gnomADg_FIN_AF|gnomADg_MID_AF|gnomADg_NFE_AF|gnomADg_REMAINING_AF|gnomADg_SAS_AF|CLIN_SIG|SOMATIC|PHENO|CHECK_REF|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE|TRANSCRIPTION_FACTORS|NearestExonJB|MaxEntScan_alt|MaxEntScan_diff|MaxEntScan_ref'
),
},

Expand Down
1 change: 1 addition & 0 deletions bolt/workflows/other/cancer_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@


import click
import logging


from ... import util
Expand Down
3 changes: 3 additions & 0 deletions bolt/workflows/smlv_germline/report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,11 +4,14 @@


import click
import logging


from ... import util
from ...common import pcgr

logger = logging.getLogger(__name__)


@click.command(name='report')
@click.pass_context
Expand Down
1 change: 1 addition & 0 deletions bolt/workflows/smlv_somatic/filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
import logging

import cyvcf2
import logging


from ... import util
Expand Down
4 changes: 4 additions & 0 deletions bolt/workflows/smlv_somatic/report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,14 @@
import click
import cyvcf2
import yaml
import logging


from ... import util
from ...common import constants
from ...common import pcgr
from ...logging_config import setup_logging
logger = logging.getLogger(__name__)


@click.command(name='report')
Expand Down Expand Up @@ -129,6 +132,7 @@ def entry(ctx, **kwargs):
output_dir,
)

pcgr_output_dir = output_dir / 'pcgr'
pcgr.run_somatic(
pcgr_prep_fp,
kwargs['pcgr_data_dir'],
Expand Down
4 changes: 2 additions & 2 deletions docker/Dockerfile.pcgr
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Original file line number Diff line number Diff line change
Expand Up @@ -15,13 +15,13 @@ RUN \
conda create \
--solver libmamba \
--name pcgr \
--file https://raw.githubusercontent.com/sigven/pcgr/refs/tags/v2.2.1/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/refs/tags/v2.2.1/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

COPY ./conda/env/bolt_env.yml /tmp/
RUN \
Expand Down
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