Release 0.2.16 (#19)

* Bump version: 0.2.15 → 0.2.16

* Change hrd facultative for cancer report (#17)

* change hrd file facultatif

* fix arg position and assign default value

* fix version (#18)

* Bump gpgr version to 2.2.0

Author: qclayssen

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.15
+current_version = 0.2.16
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[a-z0-9+]+)

README.md

@@ -54,20 +54,20 @@ the software environment and dependencies. Consequently, dependencies are split
 
 | Name    | Docker image URI                    | Commands                       |
 | ---     | ---                                 | ---                            |
-| pcgr    | ghcr.io/scwatts/bolt:0.2.15-pcgr    | • `bolt smlv_germline report`<br />• `bolt smlv_somatic annotate`<br />• `bolt smlv_somatic report`<br /> |
-| gpgr    | ghcr.io/scwatts/bolt:0.2.15-gpgr    | • `bolt other cancer_report`   |
-| snpeff  | ghcr.io/scwatts/bolt:0.2.15-snpeff  | • `bolt sv_somatic annotate`   |
-| circos  | ghcr.io/scwatts/bolt:0.2.15-circos  | • `bolt other purple_baf_plot` |
-| multiqc | ghcr.io/scwatts/bolt:0.2.15-multiqc | • `bolt other multiqc_report`  |
-| base    | ghcr.io/scwatts/bolt:0.2.15         | • `bolt smlv_germline prepare`<br />• `bolt smlv_somatic rescue`<br />• `bolt smlv_somatic filter`<br />• `bolt sv_somatic prioritise`<br /> |
+| pcgr    | ghcr.io/scwatts/bolt:0.2.16-pcgr    | • `bolt smlv_germline report`<br />• `bolt smlv_somatic annotate`<br />• `bolt smlv_somatic report`<br /> |
+| gpgr    | ghcr.io/scwatts/bolt:0.2.16-gpgr    | • `bolt other cancer_report`   |
+| snpeff  | ghcr.io/scwatts/bolt:0.2.16-snpeff  | • `bolt sv_somatic annotate`   |
+| circos  | ghcr.io/scwatts/bolt:0.2.16-circos  | • `bolt other purple_baf_plot` |
+| multiqc | ghcr.io/scwatts/bolt:0.2.16-multiqc | • `bolt other multiqc_report`  |
+| base    | ghcr.io/scwatts/bolt:0.2.16         | • `bolt smlv_germline prepare`<br />• `bolt smlv_somatic rescue`<br />• `bolt smlv_somatic filter`<br />• `bolt sv_somatic prioritise`<br /> |
 
 ## Usage
 
 Given the nature of software dependencies required, it is strongly recommended to run `bolt` commands via the existing
 [Docker images](#docker-images):
 
 ```bash
-docker run -ti -v $(pwd):$(pwd) -w $(pwd) ghcr.io/scwatts/bolt:0.2.15 \
+docker run -ti -v $(pwd):$(pwd) -w $(pwd) ghcr.io/scwatts/bolt:0.2.16 \
   bolt smlv_somatic filter \
     --tumor_name tumor_sample \
     --vcf_fp tumor_sample.vcf.gz \

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 +62,11 @@ 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
+    dragen_hrd_arg = ''
+    if kwargs['dragen_hrd_fp']:
+        dragen_hrd_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}"
+
     # Run gpgr canrep
     command = fr'''
         gpgr.R canrep \
@@ -88,15 +93,15 @@ 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']} \
+            {dragen_hrd_arg} \
             --bcftools_stats {kwargs['smlv_somatic_bcftools_stats_fp']} \
             \
             --key_genes {kwargs['cancer_genes_fp']} \
             --oncokb_genes {kwargs['oncokb_genes_fp']} \
             \
             --img_dir {output_image_dir}/ \
             --result_outdir {output_table_dir}/ \
-            --out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html
+            --out_file {output_dir}/{kwargs['tumor_name']}.cancer_report.html
     '''
     util.execute_command(command)
 

pyproject.toml

@@ -8,7 +8,7 @@ include = ["bolt*"]
 
 [project]
 name = "bolt"
-version = "0.2.15"
+version = "0.2.16"
 authors = [
   {name = "Stephen Watts", email = "[email protected]"},
 ]