From 054274f51086acde6a479725896f08b43e402a8b Mon Sep 17 00:00:00 2001 From: Quentin Clayssen Date: Mon, 22 Sep 2025 17:02:28 +1000 Subject: [PATCH 1/8] change hrd file facultatif --- bolt/workflows/other/cancer_report.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index 0799cd1..36683d9 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -29,7 +29,7 @@ @click.option('--purple_dir', required=True, type=click.Path(exists=True)) @click.option('--virusbreakend_dir', required=True, type=click.Path(exists=True)) -@click.option('--dragen_hrd_fp', required=True, type=click.Path(exists=True)) +@click.option('--dragen_hrd_fp', required=False, type=click.Path(exists=True)) @click.option('--cancer_genes_fp', required=True, type=click.Path(exists=True)) @click.option('--oncokb_genes_fp', required=True, type=click.Path(exists=True)) @@ -62,6 +62,10 @@ def entry(ctx, **kwargs): batch_name = f'{kwargs["subject_name"]}_{kwargs["tumor_name"]}' output_table_dir = output_dir / 'cancer_report_tables' + # Optional dragen hrd argument + if kwargs['dragen_hrd_fp']: + hrdetect_line = f'--dragen_hrd {kwargs['dragen_hrd_fp']}' + # Run gpgr canrep command = fr''' gpgr.R canrep \ @@ -88,7 +92,6 @@ def entry(ctx, **kwargs): --virusbreakend_tsv {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf.summary.tsv \ --virusbreakend_vcf {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf \ \ - --dragen_hrd {kwargs['dragen_hrd_fp']} \ --bcftools_stats {kwargs['smlv_somatic_bcftools_stats_fp']} \ \ --key_genes {kwargs['cancer_genes_fp']} \ @@ -97,6 +100,7 @@ def entry(ctx, **kwargs): --img_dir {output_image_dir}/ \ --result_outdir {output_table_dir}/ \ --out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html + {hrdetect_line}\ ''' util.execute_command(command) From 666398374638135f5cb7dc09853723dfd8fd49bf Mon Sep 17 00:00:00 2001 From: Quentin Clayssen Date: Mon, 22 Sep 2025 19:14:45 +1000 Subject: [PATCH 2/8] fix name variable and lint --- bolt/workflows/other/cancer_report.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index 36683d9..43dbc3a 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -64,7 +64,7 @@ def entry(ctx, **kwargs): # Optional dragen hrd argument if kwargs['dragen_hrd_fp']: - hrdetect_line = f'--dragen_hrd {kwargs['dragen_hrd_fp']}' + hrdetect_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}" # Run gpgr canrep command = fr''' @@ -100,7 +100,7 @@ def entry(ctx, **kwargs): --img_dir {output_image_dir}/ \ --result_outdir {output_table_dir}/ \ --out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html - {hrdetect_line}\ + {hrdetect_arg}\ ''' util.execute_command(command) From 580d9bdd2d86318e20e4a7aa748624898d55d621 Mon Sep 17 00:00:00 2001 From: Quentin Clayssen Date: Tue, 23 Sep 2025 10:44:08 +1000 Subject: [PATCH 3/8] fix typo --- bolt/workflows/other/cancer_report.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index 43dbc3a..793cad1 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -100,7 +100,7 @@ def entry(ctx, **kwargs): --img_dir {output_image_dir}/ \ --result_outdir {output_table_dir}/ \ --out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html - {hrdetect_arg}\ + {hrdetect_arg} \ ''' util.execute_command(command) From d34a7c28d35b16acdb1512cb0ed9c80ec0c13f8c Mon Sep 17 00:00:00 2001 From: Quentin Clayssen Date: Tue, 23 Sep 2025 12:01:01 +1000 Subject: [PATCH 4/8] typo again ...... --- bolt/workflows/other/cancer_report.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index 793cad1..c3657a2 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -96,11 +96,11 @@ def entry(ctx, **kwargs): \ --key_genes {kwargs['cancer_genes_fp']} \ --oncokb_genes {kwargs['oncokb_genes_fp']} \ + {hrdetect_arg} \ \ --img_dir {output_image_dir}/ \ --result_outdir {output_table_dir}/ \ - --out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html - {hrdetect_arg} \ + --out_file {output_dir}/{kwargs['tumor_name']}.cancer_report.html ''' util.execute_command(command) From bbb82a16272d6d401f3767a7054747c82dd9bda5 Mon Sep 17 00:00:00 2001 From: Quentin Clayssen Date: Tue, 23 Sep 2025 15:48:56 +1000 Subject: [PATCH 5/8] fix arg position and assign default value --- bolt/workflows/other/cancer_report.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index c3657a2..5cc0209 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -63,6 +63,7 @@ def entry(ctx, **kwargs): output_table_dir = output_dir / 'cancer_report_tables' # Optional dragen hrd argument + hrdetect_arg = '' if kwargs['dragen_hrd_fp']: hrdetect_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}" @@ -92,11 +93,11 @@ def entry(ctx, **kwargs): --virusbreakend_tsv {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf.summary.tsv \ --virusbreakend_vcf {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf \ \ + {hrdetect_arg} \ --bcftools_stats {kwargs['smlv_somatic_bcftools_stats_fp']} \ \ --key_genes {kwargs['cancer_genes_fp']} \ --oncokb_genes {kwargs['oncokb_genes_fp']} \ - {hrdetect_arg} \ \ --img_dir {output_image_dir}/ \ --result_outdir {output_table_dir}/ \ From df641b2bf361f986996026eddf0a38eacdbb6744 Mon Sep 17 00:00:00 2001 From: Quentin Clayssen <37511834+qclayssen@users.noreply.github.com> Date: Tue, 23 Sep 2025 17:00:22 +1000 Subject: [PATCH 6/8] fix version (#18) --- .bumpversion.cfg | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 977b262..c5ffb18 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 0.2.14 +current_version = 0.2.15 commit = True tag = False parse = (?P\d+)\.(?P\d+)\.(?P[a-z0-9+]+) From c2cdbdd70e7dde392781c3c00663b18d5681b7d0 Mon Sep 17 00:00:00 2001 From: Quentin Clayssen Date: Wed, 24 Sep 2025 14:45:11 +1000 Subject: [PATCH 7/8] Bump gpgr version to 2.2.0 --- docker/Dockerfile.gpgr | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/Dockerfile.gpgr b/docker/Dockerfile.gpgr index b8504e9..f1835d3 100644 --- a/docker/Dockerfile.gpgr +++ b/docker/Dockerfile.gpgr @@ -18,7 +18,7 @@ RUN \ RUN \ conda install --prefix /env/ \ - 'r-gpgr ==2.1.3' \ + 'r-gpgr ==2.2.0' \ 'r-sigrap ==0.1.1' \ 'bioconductor-bsgenome.hsapiens.ucsc.hg38 ==1.4.5' \ 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene ==3.16.0' \ From f3b2502f2118bfc03dd339f947c513e4f7415e7e Mon Sep 17 00:00:00 2001 From: Quentin Clayssen Date: Wed, 1 Oct 2025 11:20:44 +1000 Subject: [PATCH 8/8] fix hrd file variable name --- bolt/workflows/other/cancer_report.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bolt/workflows/other/cancer_report.py b/bolt/workflows/other/cancer_report.py index 5cc0209..983f596 100644 --- a/bolt/workflows/other/cancer_report.py +++ b/bolt/workflows/other/cancer_report.py @@ -63,9 +63,9 @@ def entry(ctx, **kwargs): output_table_dir = output_dir / 'cancer_report_tables' # Optional dragen hrd argument - hrdetect_arg = '' + dragen_hrd_arg = '' if kwargs['dragen_hrd_fp']: - hrdetect_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}" + dragen_hrd_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}" # Run gpgr canrep command = fr''' @@ -93,7 +93,7 @@ def entry(ctx, **kwargs): --virusbreakend_tsv {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf.summary.tsv \ --virusbreakend_vcf {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf \ \ - {hrdetect_arg} \ + {dragen_hrd_arg} \ --bcftools_stats {kwargs['smlv_somatic_bcftools_stats_fp']} \ \ --key_genes {kwargs['cancer_genes_fp']} \