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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
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.bumpversion.cfg

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

README.md

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

bolt/workflows/other/cancer_report.py

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@click.option('--purple_dir', required=True, type=click.Path(exists=True))
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@click.option('--virusbreakend_dir', required=True, type=click.Path(exists=True))
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@click.option('--dragen_hrd_fp', required=True, type=click.Path(exists=True))
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@click.option('--dragen_hrd_fp', required=False, type=click.Path(exists=True))
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@click.option('--cancer_genes_fp', required=True, type=click.Path(exists=True))
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@click.option('--oncokb_genes_fp', required=True, type=click.Path(exists=True))
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batch_name = f'{kwargs["subject_name"]}_{kwargs["tumor_name"]}'
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output_table_dir = output_dir / 'cancer_report_tables'
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# Optional dragen hrd argument
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dragen_hrd_arg = ''
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if kwargs['dragen_hrd_fp']:
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dragen_hrd_arg = f"--dragen_hrd {kwargs['dragen_hrd_fp']}"
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# Run gpgr canrep
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command = fr'''
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gpgr.R canrep \
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--virusbreakend_tsv {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf.summary.tsv \
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--virusbreakend_vcf {kwargs['virusbreakend_dir']}/{kwargs['tumor_name']}.virusbreakend.vcf \
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\
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--dragen_hrd {kwargs['dragen_hrd_fp']} \
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{dragen_hrd_arg} \
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--bcftools_stats {kwargs['smlv_somatic_bcftools_stats_fp']} \
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\
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--key_genes {kwargs['cancer_genes_fp']} \
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--oncokb_genes {kwargs['oncokb_genes_fp']} \
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\
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--img_dir {output_image_dir}/ \
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--result_outdir {output_table_dir}/ \
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--out_file {output_dir}/{kwargs["tumor_name"]}.cancer_report.html
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--out_file {output_dir}/{kwargs['tumor_name']}.cancer_report.html
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'''
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util.execute_command(command)
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pyproject.toml

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[project]
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name = "bolt"
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version = "0.2.15"
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version = "0.2.16"
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authors = [
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{name = "Stephen Watts", email = "[email protected]"},
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]

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