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Merged
merged 8 commits into from
Oct 7, 2025
+26 −16
Merged

pcgr 2.2.1 for sash #17

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a2b78c8
add ref data for pcgr 2.2.1
qclayssen Jun 27, 2025
daee658
add vep path pcgr
qclayssen Jun 27, 2025
5f8f3a3
edit refdata path for vep pcgr
qclayssen Jun 30, 2025
47c9b37
update pcgr report name name
qclayssen Jul 3, 2025
39774fd
change path VEP ref data
qclayssen Jul 21, 2025
5f2f74e
update container version
qclayssen Jul 21, 2025
6fc648b
remove VEP version
qclayssen Aug 29, 2025
401d2c8
change bolt version to test
qclayssen Oct 3, 2025
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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -57,7 +57,7 @@ process {

if (fp.equals('versions.yml')) {
return null
} else if (fp.matches('output/.*.pcgr_acmg.grch38.html')) {
} else if (fp.matches('output/.*.pcgr.grch38.html')) {
return "${meta.key}/${meta.tumor_id}.pcgr.html"
} else {
def fp_out = fp.replaceFirst(/output\//, '')
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5 changes: 3 additions & 2 deletions conf/refdata.config
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Expand Up @@ -4,7 +4,7 @@ params {
umccr_reference_data = '2--0'
hmf_reference_data = 'hmf_pipeline_resources.38_v2.2.0--3'

pcgr = '20220203'
pcgr = '20250314'
snpeff = '5_1'

oncokb = '4.12'
Expand All @@ -20,7 +20,8 @@ params {
}

miscdata_paths {
pcgr_dir = "databases/pcgr/v${params.data_versions.pcgr}/"
pcgr_dir = "databases/pcgr/${params.data_versions.pcgr}/"
vep_dir = "databases/pcgr/VEP/"
snpeff_dir = "databases/snpeff/v${params.data_versions.snpeff}/"

oncokb_genes = "databases/oncokb/v${params.data_versions.oncokb}/cancerGeneList.txt"
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2 changes: 1 addition & 1 deletion modules/local/bolt/other/multiqc_report/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BOLT_OTHER_MULTIQC_REPORT {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17-multiqc'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3-multiqc'

input:
tuple val(meta), path(input_files)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bolt/other/purple_baf_plot/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BOLT_OTHER_PURPLE_BAF_PLOT {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17-circos'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3-circos'

input:
tuple val(meta), path(purple_dir)
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2 changes: 1 addition & 1 deletion modules/local/bolt/smlv_germline/prepare/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BOLT_SMLV_GERMLINE_PREPARE {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3'

input:
tuple val(meta), path(smlv_vcf)
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4 changes: 3 additions & 1 deletion modules/local/bolt/smlv_germline/report/main.nf
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Expand Up @@ -2,12 +2,13 @@ process BOLT_SMLV_GERMLINE_REPORT {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3-pcgr'

input:
tuple val(meta), path(smlv_vcf), path(smlv_unfiltered_vcf)
path germline_predisposition_panel_genes
path pcgr_data_dir
path vep_dir

output:
tuple val(meta), path("output/*.variant_counts_type.yaml"), emit: counts_type
Expand All @@ -32,6 +33,7 @@ process BOLT_SMLV_GERMLINE_REPORT {
--pcgrr_conda pcgrr \\
--germline_panel_list_fp ${germline_predisposition_panel_genes} \\
--pcgr_data_dir ${pcgr_data_dir} \\
--vep_dir ${vep_dir} \\
--threads ${task.cpus} \\
--output_dir output/

Expand Down
4 changes: 3 additions & 1 deletion modules/local/bolt/smlv_somatic/annotate/main.nf
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Expand Up @@ -2,14 +2,15 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3-pcgr'

input:
tuple val(meta), path(smlv_vcf)
path somatic_driver_panel_regions_gene
path annotations_dir
path pon_dir
path pcgr_data_dir
path vep_dir

output:
tuple val(meta), path("output/${meta.tumor_id}.annotations.vcf.gz"), emit: vcf
Expand All @@ -30,6 +31,7 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
--annotations_dir ${annotations_dir} \\
--pon_dir ${pon_dir} \\
--pcgr_data_dir ${pcgr_data_dir} \\
--vep_dir ${vep_dir} \\
--pcgr_conda pcgr \\
--pcgrr_conda pcgrr \\
--threads ${task.cpus} \\
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bolt/smlv_somatic/filter/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_FILTER {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3'

input:
tuple val(meta), path(smlv_vcf)
Expand Down
10 changes: 6 additions & 4 deletions modules/local/bolt/smlv_somatic/report/main.nf
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Expand Up @@ -2,11 +2,12 @@ process BOLT_SMLV_SOMATIC_REPORT {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3-pcgr'

input:
tuple val(meta), path(smlv_vcf), path(smlv_filters_vcf), path(smlv_dragen_vcf), path(purple_purity)
path pcgr_data_dir
path vep_dir
path somatic_driver_panel_regions_coding
path giab_regions
path genome_fasta
Expand All @@ -19,7 +20,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
tuple val(meta), path("output/*.variant_counts_type.yaml") , emit: counts_type
tuple val(meta), path("output/*.variant_counts_process.json"), emit: counts_process
path 'output/pcgr/' , emit: pcgr_dir
path "output/*.pcgr_acmg.grch38.html" , emit: pcgr_report
path "output/*.pcgr.grch38.html" , emit: pcgr_report
path 'versions.yml' , emit: versions

when:
Expand All @@ -40,6 +41,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
--pcgr_conda pcgr \\
--pcgrr_conda pcgrr \\
--pcgr_data_dir ${pcgr_data_dir} \\
--vep_dir ${vep_dir} \\
--purple_purity_fp ${purple_purity} \\
\\
--cancer_genes_fp ${somatic_driver_panel_regions_coding} \\
Expand All @@ -49,7 +51,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
--threads ${task.cpus} \\
--output_dir output/

mv output/pcgr/${meta.tumor_id}.pcgr_acmg.grch38.html output/
mv output/pcgr/${meta.tumor_id}.pcgr.grch38.html output/

cat <<-END_VERSIONS > versions.yml
"${task.process}":
Expand All @@ -66,7 +68,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
touch output/${meta.tumor_id}.somatic.variant_counts_type.yaml
touch output/${meta.tumor_id}.somatic.variant_counts_process.json
touch output/${meta.tumor_id}.somatic.bcftools_stats.txt
touch output/${meta.tumor_id}.pcgr_acmg.grch38.html
touch output/${meta.tumor_id}.pcgr.grch38.html
echo -e '${task.process}:\\n stub: noversions\\n' > versions.yml
"""
}
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bolt/smlv_somatic/rescue/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_RESCUE {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3'

input:
tuple val(meta), path(smlv_vcf), path(smlv_tbi), path(sage_smlv_vcf), path(sage_smlv_tbi)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bolt/sv_somatic/annotate/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BOLT_SV_SOMATIC_ANNOTATE {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17-snpeff'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3-snpeff'

input:
tuple val(meta), path(sv_vcf), path(cnv_tsv)
Expand Down
2 changes: 1 addition & 1 deletion modules/local/bolt/sv_somatic/prioritise/main.nf
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Expand Up @@ -2,7 +2,7 @@ process BOLT_SV_SOMATIC_PRIORITISE {
tag "${meta.id}"
label 'process_low'

container 'ghcr.io/umccr/bolt:0.2.17'
container 'ghcr.io/umccr/bolt:0.3.0-pcgr-v2.2.5-3'

input:
tuple val(meta), path(sv_vcf)
Expand Down
3 changes: 3 additions & 0 deletions workflows/sash.nf
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Expand Up @@ -152,6 +152,7 @@ workflow SASH {
umccr_data.annotations_dir,
misc_data.pon_dir,
misc_data.pcgr_dir,
misc_data.vep_dir
)

ch_versions = ch_versions.mix(BOLT_SMLV_SOMATIC_ANNOTATE.out.versions)
Expand Down Expand Up @@ -304,6 +305,7 @@ workflow SASH {
BOLT_SMLV_SOMATIC_REPORT(
ch_smlv_somatic_report_inputs,
misc_data.pcgr_dir,
misc_data.vep_dir,
umccr_data.somatic_panel_regions_cds,
hmf_data.sage_highconf_regions,
genome.fasta,
Expand All @@ -330,6 +332,7 @@ workflow SASH {
ch_smlv_germline_report_inputs,
umccr_data.germline_panel_genes,
misc_data.pcgr_dir,
misc_data.vep_dir
)

ch_versions = ch_versions.mix(BOLT_SMLV_GERMLINE_REPORT.out.versions)
Expand Down