Release 0.6.0 (#9)

qclayssen · web-flow · commit e81bb21058c2 · 2025-06-19T17:20:58.000+10:00
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.0
+current_version = 0.6.0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[a-z0-9+]+)
diff --git a/conf/modules.config b/conf/modules.config
@@ -175,7 +175,7 @@ process {
         ]
     }
 
-    withName: '.*:LINX_ANNOTATION:(?:GERMLINE|SOMATIC)|.*:LINX_PLOTTING:VISUALISER' {
+    withName: '.*:LINX_ANNOTATION:(?:GERMLINE|SOMATIC)|.*:LINX_PLOTTING:LINX_VISUALISER' {
         ext.jarPath = '/opt/linx/linx.jar'
     }
 
@@ -195,7 +195,7 @@ process {
         ]
     }
 
-    withName: '.*:LINX_PLOTTING:VISUALISER' {
+    withName: '.*:LINX_PLOTTING:LINX_VISUALISER' {
         ext.circosPath = '/opt/conda/bin/circos'
         publishDir = [
             path: { "${params.outdir}" },
@@ -204,7 +204,7 @@ process {
         ]
     }
 
-    withName: '.*:LINX_PLOTTING:REPORT' {
+    withName: '.*:LINX_PLOTTING:LINXREPORT' {
         publishDir = [
             path: { "${params.outdir}" },
             mode: params.publish_dir_mode,
diff --git a/modules/local/bolt/other/cancer_report/main.nf b/modules/local/bolt/other/cancer_report/main.nf
@@ -2,7 +2,7 @@ process BOLT_OTHER_CANCER_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.14-dev-gpgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-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)
diff --git a/modules/local/bolt/other/multiqc_report/main.nf b/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:0.2.14-dev-multiqc'
+    container 'ghcr.io/umccr/bolt:0.2.14-multiqc'
 
     input:
     tuple val(meta), path(input_files)
diff --git a/modules/local/bolt/other/purple_baf_plot/main.nf b/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:0.2.14-dev-circos'
+    container 'ghcr.io/umccr/bolt:0.2.14-circos'
 
     input:
     tuple val(meta), path(purple_dir)
diff --git a/modules/local/bolt/smlv_germline/prepare/main.nf b/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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     input:
     tuple val(meta), path(smlv_vcf)
diff --git a/modules/local/bolt/smlv_germline/report/main.nf b/modules/local/bolt/smlv_germline/report/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_GERMLINE_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_unfiltered_vcf)
diff --git a/modules/local/bolt/smlv_somatic/annotate/main.nf b/modules/local/bolt/smlv_somatic/annotate/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_ANNOTATE {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf)
diff --git a/modules/local/bolt/smlv_somatic/filter/main.nf b/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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     input:
     tuple val(meta), path(smlv_vcf)
diff --git a/modules/local/bolt/smlv_somatic/report/main.nf b/modules/local/bolt/smlv_somatic/report/main.nf
@@ -2,7 +2,7 @@ process BOLT_SMLV_SOMATIC_REPORT {
     tag "${meta.id}"
     label 'process_low'
 
-    container 'ghcr.io/umccr/bolt:0.2.14-dev-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_filters_vcf), path(smlv_dragen_vcf), path(purple_purity)
diff --git a/modules/local/bolt/smlv_somatic/rescue/main.nf b/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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_tbi), path(sage_smlv_vcf), path(sage_smlv_tbi)
diff --git a/modules/local/bolt/sv_somatic/annotate/main.nf b/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:0.2.14-dev-snpeff'
+    container 'ghcr.io/umccr/bolt:0.2.14-snpeff'
 
     input:
     tuple val(meta), path(sv_vcf), path(cnv_tsv)
diff --git a/modules/local/bolt/sv_somatic/prioritise/main.nf b/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:0.2.14-dev'
+    container 'ghcr.io/umccr/bolt:0.2.14'
 
     input:
     tuple val(meta), path(sv_vcf)
diff --git a/nextflow.config b/nextflow.config
@@ -168,12 +168,12 @@ dag {
 
 manifest {
     name            = 'umccr/sash'
-    author          = """Stephen Watts"""
+    author          = """Stephen Watts, Quentin Clayssen"""
     homePage        = 'https://github.com/umccr/sash'
     description     = """Cancer WGTS post-processing pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.6'
-    version         = '0.5.0'
+    version         = '0.6.0'
     doi             = ''
 }
 
diff --git a/subworkflows/local/linx_plotting.nf b/subworkflows/local/linx_plotting.nf
@@ -2,8 +2,8 @@
 // LINX plotting visualises clusters structural variants
 //
 
-include { LINXREPORT as REPORT          } from '../../modules/local/linxreport/main'
-include { LINX_VISUALISER as VISUALISER } from '../../modules/local/linx/visualiser/main'
+include { LINXREPORT } from '../../modules/local/linxreport/main'
+include { LINX_VISUALISER } from '../../modules/local/linx/visualiser/main'
 
 workflow LINX_PLOTTING {
     take:
@@ -32,15 +32,15 @@ workflow LINX_PLOTTING {
                 return [meta_linx, anno_dir]
             }
 
-        VISUALISER(
+        LINX_VISUALISER(
             ch_linx_visualiser_inputs,
             genome_version,
             ensembl_data_resources,
         )
 
-        ch_versions = ch_versions.mix(VISUALISER.out.versions)
+        ch_versions = ch_versions.mix(LINX_VISUALISER.out.versions)
 
-        ch_visualiser_out = WorkflowSash.restoreMeta(VISUALISER.out.plots, ch_inputs)
+        ch_visualiser_out = WorkflowSash.restoreMeta(LINX_VISUALISER.out.plots, ch_inputs)
 
         // Create inputs and create process-specific meta
         // channel: [ meta_linxreport, linx_annotation_dir, linx_plot_dir ]
@@ -57,11 +57,11 @@ workflow LINX_PLOTTING {
                 return [meta_linxreport, anno_dir, plot_dir]
             }
 
-        REPORT(
+        LINXREPORT(
             ch_linxreport_inputs,
         )
 
-        ch_versions = ch_versions.mix(REPORT.out.versions)
+        ch_versions = ch_versions.mix(LINXREPORT.out.versions)
 
     emit:
         plot_dir = ch_visualiser_out // channel: [ meta, plot_dir ]

Original file line number	Diff line number	Diff line change
`@@ -175,7 +175,7 @@ process {`
`175`	`175`	`]`
`176`	`176`	`}`
`177`	`177`
`178`		`- withName: '.:LINX_ANNOTATION:(?:GERMLINE\|SOMATIC)\|.:LINX_PLOTTING:VISUALISER' {`
	`178`	`+ withName: '.:LINX_ANNOTATION:(?:GERMLINE\|SOMATIC)\|.:LINX_PLOTTING:LINX_VISUALISER' {`
`179`	`179`	`ext.jarPath = '/opt/linx/linx.jar'`
`180`	`180`	`}`
`181`	`181`
`@@ -195,7 +195,7 @@ process {`
`195`	`195`	`]`
`196`	`196`	`}`
`197`	`197`
`198`		`- withName: '.*:LINX_PLOTTING:VISUALISER' {`
	`198`	`+ withName: '.*:LINX_PLOTTING:LINX_VISUALISER' {`
`199`	`199`	`ext.circosPath = '/opt/conda/bin/circos'`
`200`	`200`	`publishDir = [`
`201`	`201`	`path: { "${params.outdir}" },`
`@@ -204,7 +204,7 @@ process {`
`204`	`204`	`]`
`205`	`205`	`}`
`206`	`206`
`207`		`- withName: '.*:LINX_PLOTTING:REPORT' {`
	`207`	`+ withName: '.*:LINX_PLOTTING:LINXREPORT' {`
`208`	`208`	`publishDir = [`
`209`	`209`	`path: { "${params.outdir}" },`
`210`	`210`	`mode: params.publish_dir_mode,`