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fix: umi coverage qc #1490

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merged 6 commits into from
Oct 17, 2024
Merged

fix: umi coverage qc #1490

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fedcb8f
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Oct 17, 2024
2007528
Merge branch 'develop' of github.com:Clinical-Genomics/BALSAMIC into …
mathiasbio Oct 17, 2024
fd3d549
rename umi
mathiasbio Oct 17, 2024
f9751c6
changelog
mathiasbio Oct 17, 2024
c571b4d
fix umi qc rules
mathiasbio Oct 17, 2024
23156ec
fix
mathiasbio Oct 17, 2024
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6 changes: 3 additions & 3 deletions BALSAMIC/snakemake_rules/umi/sentieon_consensuscall.rule
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Expand Up @@ -92,7 +92,7 @@ rule sentieon_consensusfilter_umi:
input:
umi_dir + "{sample_type}.{sample}.consensuscalled_umi.bam"
output:
umi_dir + "{sample_type}.{sample}.consensusfiltered_umi.bam"
umi_dir + "{sample_type}.{sample}_consensusfiltered_umi.bam"
benchmark:
Path(benchmark_dir, "sentieon_consensusfilter_umi_{sample_type}_{sample}.tsv").as_posix()
singularity:
Expand All @@ -119,7 +119,7 @@ samtools index {output};

rule bam_compress_tumor_umi:
input:
bam = umi_dir + "tumor.{sample}.consensusfiltered_umi.bam",
bam = umi_dir + "tumor.{sample}_consensusfiltered_umi.bam",
fasta = config_model.reference["reference_genome"]
output:
cram = umi_dir + "tumor.{sample}.consensusfiltered_umi.cram",
Expand All @@ -143,7 +143,7 @@ samtools index {output.cram};
if config['analysis']['analysis_type'] == "paired":
rule bam_compress_normal_umi:
input:
bam = umi_dir + "normal.{sample}.consensusfiltered_umi.bam",
bam = umi_dir + "normal.{sample}_consensusfiltered_umi.bam",
fasta = config_model.reference["reference_genome"]
output:
cram = umi_dir + "normal.{sample}.consensusfiltered_umi.cram"
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1 change: 1 addition & 0 deletions CHANGELOG.rst
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Expand Up @@ -36,6 +36,7 @@ Changed:
* Lowered maximal SOR for TNscope in TGA tumor only cases from 3 to 2.7 https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
* Fixed TNscope research VCF filters to either PASS or triallelic site https://github.com/Clinical-Genomics/BALSAMIC/pull/1475
* Increased maximal amount of redirects for lychee test following links in docs to 10 https://github.com/Clinical-Genomics/BALSAMIC/pull/1488
* Renamed UMI consensusfiltered bamfile to be picked up by multiqc https://github.com/Clinical-Genomics/BALSAMIC/pull/1490

Removed:
^^^^^^^^
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