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fix: cram file hk tags #1307

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Nov 1, 2023
Merged

fix: cram file hk tags #1307

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75aec77
remove final bam suffix
mathiasbio Oct 31, 2023
7b40b4f
fix bug
mathiasbio Oct 31, 2023
b4f0f76
Merge branch 'develop' into fix_cram_file_hk_tags
mathiasbio Nov 1, 2023
dae58ff
changelog
mathiasbio Nov 1, 2023
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16 changes: 8 additions & 8 deletions BALSAMIC/snakemake_rules/align/bam_compress.rule
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Original file line number Diff line number Diff line change
Expand Up @@ -6,18 +6,18 @@ rule bam_compress_tumor:
bam = lambda wildcards: config_model.get_final_bam_name(bam_dir = bam_dir, sample_name = wildcards.sample),
fasta = config_model.reference["reference_genome"]
output:
cram = Path(bam_dir + "tumor.{sample}.{final_bam_suffix}.cram").as_posix()
cram = Path(bam_dir + "tumor.{sample}.cram").as_posix()
benchmark:
Path(benchmark_dir, "bam_compress_{final_bam_suffix}_{sample}.tsv").as_posix()
Path(benchmark_dir, "bam_compress_tumor_{sample}.tsv").as_posix()
singularity:
Path(singularity_image, config["bioinfo_tools"].get("compress") + ".sif").as_posix()
params:
sample_id = "{sample}",
housekeeper_id= {"id": case_id, "tags": "tumor"}
housekeeper_id= {"id": "{sample}", "tags": "tumor"}
threads:
get_threads(cluster_config, "bam_compress")
message:
"Compressing bam ({final_bam_suffix}) to cram for {params.sample_id}"
"Compressing bam to cram for {params.sample_id}"
shell:
"""
samtools view -h -T {input.fasta} --threads {threads} -C -o {output.cram} {input.bam};
Expand All @@ -29,18 +29,18 @@ rule bam_compress_normal:
bam = lambda wildcards: config_model.get_final_bam_name(bam_dir = bam_dir, sample_name = wildcards.sample),
fasta = config_model.reference["reference_genome"]
output:
cram = Path(bam_dir, "normal.{sample}.{final_bam_suffix}.cram").as_posix()
cram = Path(bam_dir, "normal.{sample}.cram").as_posix()
benchmark:
Path(benchmark_dir, "bam_compress_{final_bam_suffix}_{sample}.tsv").as_posix()
Path(benchmark_dir, "bam_compress_normal_{sample}.tsv").as_posix()
singularity:
Path(singularity_image, config["bioinfo_tools"].get("compress") + ".sif").as_posix()
params:
sample_id = "{sample}",
housekeeper_id= {"id": case_id, "tags": "normal"}
housekeeper_id= {"id": "{sample}", "tags": "normal"}
threads:
get_threads(cluster_config, "bam_compress")
message:
"Compressing bam ({final_bam_suffix}) to cram for {params.sample_id}"
"Compressing bam to cram for {params.sample_id}"
shell:
"""
samtools view -h -T {input.fasta} --threads {threads} -C -o {output.cram} {input.bam};
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8 changes: 2 additions & 6 deletions BALSAMIC/snakemake_rules/quality_control/multiqc.rule
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Expand Up @@ -7,18 +7,14 @@ multiqc_input.append(qc_dir + "tumor.{}.dedup.metrics".format(tumor_sample))
multiqc_input.extend(expand(bam_dir + "{sample}.samtools.{stats}.txt",
sample=sample_names, stats=['flagstats', 'idxstats', 'stats']))

if config["analysis"]["sequencing_type"] == 'wgs':
final_bam_suffix = "dedup.realign"
else:
final_bam_suffix = "dedup"

multiqc_input.extend(expand(bam_dir + "tumor.{sample}.{final_bam_suffix}.cram", sample=tumor_sample, final_bam_suffix=final_bam_suffix))
multiqc_input.extend(expand(bam_dir + "tumor.{sample}.cram", sample=tumor_sample))

# fastqc metrics
multiqc_input.extend(expand(fastqc_dir + "{fastq_file_names}_fastqc.zip", fastq_file_names=config_model.get_all_fastq_names(remove_suffix = True)))

if config['analysis']['analysis_type'] == "paired":
multiqc_input.extend(expand(bam_dir + "normal.{sample}.{final_bam_suffix}.cram", sample=normal_sample, final_bam_suffix=final_bam_suffix))
multiqc_input.extend(expand(bam_dir + "normal.{sample}.cram", sample=normal_sample))
multiqc_input.append(config_model.get_final_bam_name(bam_dir = bam_dir, sample_name = normal_sample))
multiqc_input.append(qc_dir + "somalier/somalier.pairs.tsv")
multiqc_input.append(qc_dir + "normal.{}.dedup.metrics".format(normal_sample))
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1 change: 1 addition & 0 deletions CHANGELOG.rst
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Expand Up @@ -60,6 +60,7 @@ Changed:
* Migrate Cache models to pydantic v2 https://github.com/Clinical-Genomics/BALSAMIC/pull/1274
* Made BALSAMIC compatible with multiple PON creation workflows https://github.com/Clinical-Genomics/BALSAMIC/pull/1279
* Use StrEnum from python enum https://github.com/Clinical-Genomics/BALSAMIC/pull/1303
* Renamed final cram bamfile to format [tumor/normal].LIMSID.cram https://github.com/Clinical-Genomics/BALSAMIC/pull/1307


Fixed:
Expand Down