Skip to content

Commit

Permalink
Update peak_calling_method to "lanceotron" in NonRNAOutput class
Browse files Browse the repository at this point in the history
  • Loading branch information
alsmith151 committed Apr 9, 2024
1 parent 99346d8 commit d140fdc
Show file tree
Hide file tree
Showing 3 changed files with 3 additions and 3 deletions.
2 changes: 1 addition & 1 deletion seqnado/design.py
Original file line number Diff line number Diff line change
Expand Up @@ -1047,7 +1047,7 @@ def merged_peaks(self):
assay=self.assay,
names=self.design_dataframe["merge"].unique().tolist(),
call_peaks=self.call_peaks,
peak_calling_method=self.peak_calling_method,
peak_calling_method="lanceotron",
prefix="seqnado_output/peaks/merged/",
)

Expand Down
2 changes: 1 addition & 1 deletion seqnado/workflow/rules/alignment_post_processing.smk
Original file line number Diff line number Diff line change
Expand Up @@ -204,7 +204,7 @@ def get_bam_files_for_merge(wildcards):
from seqnado.design import NormGroups
norm_groups = NormGroups.from_design(DESIGN, subset_column="merge")

sample_names = norm_groups.get_sample_names(wildcards.group)
sample_names = norm_groups.get_grouped_samples(wildcards.group)

return [
f"seqnado_output/aligned/{sample}.bam" for sample in sample_names
Expand Down
2 changes: 1 addition & 1 deletion seqnado/workflow/rules/peak_call_grouped.smk
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ rule lanceotron_no_input_consensus:
input:
bigwig="seqnado_output/bigwigs/deeptools/grouped/{group}.bigWig",
output:
peaks="seqnado_output/peaks/lanceotron/grouped/{group}.bed",
peaks="seqnado_output/peaks/grouped/lanceotron/{group}.bed",
threads: 8
log:
"seqnado_output/logs/lanceotron/{group}.log",
Expand Down

0 comments on commit d140fdc

Please sign in to comment.