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Commit 47ad6ff2 authored by Manavalan Gajapathy's avatar Manavalan Gajapathy
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fixes path for mosdepth plotting

parent da33c7c3
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......@@ -49,6 +49,10 @@ def main(outpath):
"tracking_sheet": "data/external/project_tracker/PROJECT TRACKING -CF.xlsx",
"affected": "all",
},
"CF_TLOAF_PFarrell": {
"tracking_sheet": "data/external/project_tracker/PROJECT TRACKING -CF.xlsx",
"affected": "all",
},
# "CF_TLOAF_PFarrell",
# "EDS3_unkn_DGreenspan",
# "MuscDyst_SU_MAlexander",
......
......@@ -38,12 +38,14 @@ rule mosdepth_plot:
"Running mosdepth plotting. Project: {wildcards.project}"
params:
in_dir = lambda wildcards, input: Path(input[0]).parent,
workflow_dir = Path(workflow.basedir).parent
shell:
r"""
echo "Heads up: Mosdepth-plotting is run on all samples in "{params.in_dir}"; Not just the files mentioned in the rule's input."
cd {params.in_dir}
cd {params.in_dir} # if not in directory, mosdepth uses filepath as sample name :(
python {input.script} \
--output $(basename {output}) \
*.mosdepth.global.dist.txt
--output {params.workflow_dir}/{output} \
*.mosdepth.global.dist.txt \
> {params.workflow_dir}/{log} 2>&1
"""
rule extract:
rule somalier_extract:
input:
bam = PROJECTS_PATH / "{project}" / "analysis" / "{sample}" / "bam" / "{sample}.bam",
bam_index = PROJECTS_PATH / "{project}" / "analysis" / "{sample}" / "bam" / "{sample}.bam.bai",
......@@ -24,7 +24,7 @@ rule extract:
"""
rule relate:
rule somalier_relate:
input:
extracted = lambda wildcards: expand(str(INTERIM_DIR / "somalier_extract" / wildcards.project / "{sample}.somalier"),
sample=SAMPLES[wildcards.project]),
......@@ -53,7 +53,7 @@ rule relate:
"""
rule ancestry:
rule somalier_ancestry:
input:
extracted = lambda wildcards: expand(str(INTERIM_DIR / "somalier_extract" / wildcards.project / "{sample}.somalier"),
sample=SAMPLES[wildcards.project]),
......
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