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Linting, fmt, config update
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weber8thomas committed Dec 4, 2023
1 parent d8977fe commit e90a7a5
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Showing 5 changed files with 17 additions and 12 deletions.
4 changes: 2 additions & 2 deletions config/config.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,10 @@
# --------------------------------------------------------

# MosaiCatcher version
version: 2.2.2
version: 2.2.3

# Ashleys-QC pipeline version
ashleys_pipeline_version: 2.2.2
ashleys_pipeline_version: 2.2.3

# Email for notifications about the pipeline's status
email: ""
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12 changes: 6 additions & 6 deletions workflow/Snakefile
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Expand Up @@ -19,12 +19,12 @@ if config["ashleys_pipeline"] is True:

module ashleys_qc:
snakefile:
"../../ashleys-qc-pipeline/workflow/Snakefile"
# github(
# "friendsofstrandseq/ashleys-qc-pipeline",
# path="workflow/Snakefile",
# tag=str(config["ashleys_pipeline_version"]),
# )
# "../../ashleys-qc-pipeline/workflow/Snakefile"
github(
"friendsofstrandseq/ashleys-qc-pipeline",
path="workflow/Snakefile",
tag=str(config["ashleys_pipeline_version"]),
)
config:
config

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4 changes: 3 additions & 1 deletion workflow/rules/common.smk
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,9 @@ os.environ["LC_CTYPE"] = "C"
# print(config["data_location"])

if config["ashleys_pipeline"] is True and config["genecore"] is True:
config["data_location"] = "/".join(config["data_location"].split("/")[:-1])
config["data_location"] = config["abs_path"].join(
config["data_location"].split("/")[:-1]
)


envvars:
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3 changes: 2 additions & 1 deletion workflow/rules/plots.smk
Original file line number Diff line number Diff line change
Expand Up @@ -315,7 +315,8 @@ rule scTRIP_multiplot:
"{folder}/log/scTRIP_multiplot/{sample}/{cell}/{chrom}.log",
conda:
"../envs/rtools.yaml"
container: None
container:
None
resources:
mem_mb=get_mem_mb,
shell:
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6 changes: 4 additions & 2 deletions workflow/rules/setup.smk
Original file line number Diff line number Diff line change
Expand Up @@ -20,8 +20,10 @@ rule install_BSgenome_package:
params:
selected_package=lambda wc, input: "BSgenome.{}.UCSC.{}".format(
"Mmusculus" if config["reference"] == "mm10" else "Hsapiens",
config["reference"]
) if config["reference"] in ["hg38", "hg19", "mm10"] else input.package,
config["reference"],
)
if config["reference"] in ["hg38", "hg19", "mm10"]
else input.package,
conda:
"../envs/rtools.yaml"
resources:
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