change make hrd facultative for cancer report process (#26)

* change make hrd facultative for cancer report  process

* add absolut path

* bump bolt version

* bump bolt version v0.2.16 -> 0.2.17

Author: qclayssen

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:0.2.15-gpgr'
+    container 'ghcr.io/umccr/bolt:0.2.17-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)
@@ -19,6 +19,8 @@ process BOLT_OTHER_CANCER_REPORT {
 
     script:
 
+    def dragen_hrd_arg = dragen_hrd ? "--dragen_hrd_fp \$(pwd)/${dragen_hrd}" : ''
+
     """
     # NOTE(SW): gpgr requires aboslute paths
 
@@ -42,7 +44,7 @@ process BOLT_OTHER_CANCER_REPORT {
         --purple_dir \$(pwd)/${purple_dir} \\
         --virusbreakend_dir \$(pwd)/${virusbreakend_dir} \\
         \\
-        --dragen_hrd_fp \$(pwd)/${dragen_hrd} \\
+        ${dragen_hrd_arg} \\
         \\
         --cancer_genes_fp \$(pwd)/${somatic_driver_panel} \\
         --oncokb_genes_fp \$(pwd)/${oncokb_genes} \\

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:0.2.15-multiqc'
+    container 'ghcr.io/umccr/bolt:0.2.17-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:0.2.15-circos'
+    container 'ghcr.io/umccr/bolt:0.2.17-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:0.2.15'
+    container 'ghcr.io/umccr/bolt:0.2.17'
 
     input:
     tuple val(meta), path(smlv_vcf)

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:0.2.15-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_unfiltered_vcf)

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:0.2.15-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf)

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:0.2.15'
+    container 'ghcr.io/umccr/bolt:0.2.17'
 
     input:
     tuple val(meta), path(smlv_vcf)

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:0.2.15-pcgr'
+    container 'ghcr.io/umccr/bolt:0.2.17-pcgr'
 
     input:
     tuple val(meta), path(smlv_vcf), path(smlv_filters_vcf), path(smlv_dragen_vcf), path(purple_purity)

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:0.2.15'
+    container 'ghcr.io/umccr/bolt:0.2.17'
 
     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:0.2.15-snpeff'
+    container 'ghcr.io/umccr/bolt:0.2.17-snpeff'
 
     input:
     tuple val(meta), path(sv_vcf), path(cnv_tsv)