Release/0.7.0

.nf-core.yml

@@ -1,29 +1,29 @@
 repository_type: pipeline
 lint:
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-sash_logo_light.png
-  - docs/images/nf-core-sash_logo_light.png
-  - docs/images/nf-core-sash_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
-  - .github/ISSUE_TEMPLATE/bug_report.yml
-  - .github/workflows/branch.yml
-  - .github/workflows/ci.yml
-  - .github/workflows/linting_comment.yml
-  - .github/workflows/linting.yml
-  - conf/igenomes.config
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-sash_logo_light.png
+    - docs/images/nf-core-sash_logo_light.png
+    - docs/images/nf-core-sash_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
+    - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/workflows/branch.yml
+    - .github/workflows/ci.yml
+    - .github/workflows/linting_comment.yml
+    - .github/workflows/linting.yml
+    - conf/igenomes.config
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
-  - process.cpus
-  - process.memory
-  - process.time
-  - custom_config
+    - manifest.name
+    - manifest.homePage
+    - process.cpus
+    - process.memory
+    - process.time
+    - custom_config
   multiqc_config:
-  - report_comment
+    - report_comment
   files_unchanged:
-  - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/ISSUE_TEMPLATE/bug_report.yml
   readme:
-  - nextflow_badge
+    - nextflow_badge

CHANGELOG.md

@@ -113,9 +113,9 @@ Initial release of umccr/sash, created with the [nf-core](https://nf-co.re/) tem
 
 ### Dependencies
 
-| Tool | Old | New |
-|------|-----|-----|
-| Linx | 1.25 | 2.0 |
-| Purple | 4.0.1 | 4.1.0 |
-| Bolt | — | umccr/bolt#6 |
-| GPGR | — | umccr/gpgr#88 |
+| Tool   | Old   | New           |
+| ------ | ----- | ------------- |
+| Linx   | 1.25  | 2.0           |
+| Purple | 4.0.1 | 4.1.0         |
+| Bolt   | —     | umccr/bolt#6  |
+| GPGR   | —     | umccr/gpgr#88 |

README.md

@@ -11,9 +11,9 @@ functionality.
 
 ## Table of contents
 
-* [Summary](#summary)
-* [Requirements](#requirements)
-* [Usage](#usage)
+- [Summary](#summary)
+- [Requirements](#requirements)
+- [Usage](#usage)
 
 ## Summary
 

conf/modules.config

@@ -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\//, '')
@@ -126,7 +126,30 @@ process {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/${filename}" },
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/${filename}" }
+        ]
+    }
+
+
+    withName: 'SIGRAP_HRDETECT' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/sigrap/hrdetect/${filename}" }
+        ]
+    }
+
+    withName: 'SIGRAP_MUTPAT' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> 
+                if (filename.equals('versions.yml')) {
+                    return null
+                } else {
+                    return "${meta.key}/sigrap/${filename}"
+                }
+            }
         ]
     }
 
@@ -212,4 +235,12 @@ process {
         ]
     }
 
+    withName: 'VCF2MAF' {
+        publishDir = [
+            path: { "${params.outdir}" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.key}/vcf2maf/${filename}" },
+        ]
+    }
+
 }

conf/refdata.config

@@ -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'
@@ -20,7 +20,8 @@ params {
     }
 
     miscdata_paths {
-        pcgr_dir = "databases/pcgr/v${params.data_versions.pcgr}/"
+        pcgr_dir = "databases/pcgr/pcgr_ref_data.${params.data_versions.pcgr}.grch38.tgz"
+        vep_dir = "databases/pcgr/homo_sapiens_vep_113_GRCh38.tar.gz"
         snpeff_dir = "databases/snpeff/v${params.data_versions.snpeff}/"
 
         oncokb_genes = "databases/oncokb/v${params.data_versions.oncokb}/cancerGeneList.txt"

modules/local/bolt/other/cancer_report/main.nf

@@ -2,10 +2,10 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.17-gpgr'
+    container 'docker.io/qclayssen/bolt:0.3.0-dev-14-gpgr'
 
     input:
-    tuple val(meta), path(smlv_somatic_vcf), path(smlv_somatic_bcftools_stats), path(smlv_somatic_counts_process), path(sv_somatic_tsv), path(sv_somatic_vcf), path(cnv_somatic_tsv), path(af_global), path(af_keygenes), path(purple_baf_plot), path(purple_dir), path(virusbreakend_dir), path(dragen_hrd)
+    tuple val(meta), path(smlv_somatic_vcf), path(smlv_somatic_bcftools_stats), path(smlv_somatic_counts_process), path(sv_somatic_tsv), path(sv_somatic_vcf), path(cnv_somatic_tsv), path(af_global), path(af_keygenes), path(purple_baf_plot), path(purple_dir), path(virusbreakend_dir), path(dragen_hrd), path(smlv_somatic_mutpat), path(smlv_somatic_hrdetect), path(smlv_somatic_chord)
     path somatic_driver_panel
     path oncokb_genes
 
@@ -35,6 +35,10 @@ process BOLT_OTHER_CANCER_REPORT {
         --smlv_somatic_bcftools_stats_fp \$(pwd)/${smlv_somatic_bcftools_stats} \\
         --smlv_somatic_counts_process_fp \$(pwd)/${smlv_somatic_counts_process} \\
         \\
+        --mutpat_dir \$(pwd)/${smlv_somatic_mutpat} \\
+        --hrdetect_file \$(pwd)/${smlv_somatic_hrdetect} \\
+        --chord_file \$(pwd)/${smlv_somatic_chord} \\
+        \\
         --sv_somatic_tsv_fp \$(pwd)/${sv_somatic_tsv} \\
         --sv_somatic_vcf_fp \$(pwd)/${sv_somatic_vcf} \\
         --cnv_somatic_tsv_fp \$(pwd)/${cnv_somatic_tsv} \\

modules/local/bolt/other/multiqc_report/main.nf

@@ -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-dev-20-multiqc'
 
     input:
     tuple val(meta), path(input_files)

modules/local/bolt/other/purple_baf_plot/main.nf

@@ -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-dev-20-circos'
 
     input:
     tuple val(meta), path(purple_dir)

modules/local/bolt/smlv_germline/prepare/main.nf

@@ -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-dev-20'
 
     input:
     tuple val(meta), path(smlv_vcf)

modules/local/bolt/smlv_germline/report/main.nf

@@ -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-dev-20-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
@@ -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/
 

modules/local/bolt/smlv_somatic/annotate/main.nf

@@ -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-dev-20-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
@@ -19,7 +20,7 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def chunk_size_arg = params.pcgr_variant_chunk_size ? "--pcgr_variant_chunk_size ${params.pcgr_variant_chunk_size}" : ''
 
     """
     bolt smlv_somatic annotate \\
@@ -30,10 +31,12 @@ 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} \\
-        --output_dir output/
+        --output_dir output/ \\
+        ${chunk_size_arg}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/bolt/smlv_somatic/filter/main.nf

@@ -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-dev-20'
 
     input:
     tuple val(meta), path(smlv_vcf)

modules/local/bolt/smlv_somatic/report/main.nf

@@ -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-dev-20-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
@@ -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:
@@ -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} \\
@@ -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
     "${task.process}":
@@ -66,7 +68,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
     touch output/${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
     """
 }

modules/local/bolt/smlv_somatic/rescue/main.nf

@@ -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-dev-20'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_tbi), path(sage_smlv_vcf), path(sage_smlv_tbi)

modules/local/bolt/sv_somatic/annotate/main.nf

@@ -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-dev-20-snpeff'
 
     input:
     tuple val(meta), path(sv_vcf), path(cnv_tsv)

modules/local/bolt/sv_somatic/prioritise/main.nf

@@ -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-dev-20'
 
     input:
     tuple val(meta), path(sv_vcf)

modules/local/custom/extract_tarball/main.nf

@@ -0,0 +1,33 @@
+process CUSTOM_EXTRACTTARBALL {
+    label 'process_single'
+
+    conda "conda-forge::tar=1.34"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
+        'quay.io/nf-core/ubuntu:20.04' }"
+
+    input:
+    tuple val(meta), path(tarball)
+
+    output:
+    path "${meta.id}/", emit: extracted_dir
+    path '.command.*', emit: command_files
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def strip = meta.strip_components != null ? meta.strip_components : 1
+    def target = meta.subdir ? "${meta.id}/${meta.subdir}" : "${meta.id}"
+
+    """
+    mkdir -p ${target}
+    tar ${args} -xzvf ${tarball} --strip-components ${strip} -C ${target}/
+    """
+
+    stub:
+    """
+    mkdir -p ${meta.id}/
+    """
+}

modules/local/pave/somatic/meta.yml

@@ -12,7 +12,7 @@ tools:
       description: Annotates small variant VCF with gene, transcript coding and protein effects.
       homepage: https://github.com/hartwigmedical/hmftools/tree/master/pave
       documentation: https://github.com/hartwigmedical/hmftools/tree/master/pave
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 input:
   - meta:
       type: map