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fix: correct pipeline output files #96

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Merged
kelly-sovacool merged 1 commit into from
May 5, 2025
+2 −7
Merged

fix: correct pipeline output files #96

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7 changes: 1 addition & 6 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -52,17 +52,12 @@ rule all:
#genrich peaks
expand(join(PEAKSDIR, "genrich", "{sample}.consensus.genrich.peakfiles"), sample=SAMPLES),
expand(join(PEAKSDIR, "genrich", "{sample}.replicate.genrich.peakfiles"), sample=SAMPLES),
expand(join(PEAKSDIR, "genrich", "genrich","{sample}.genrich.tn5nicksbedfiles"),sample=SAMPLES),
# roi gtf
expand(join(RESULTSDIR,"peaks","{peakcaller}","fixed_width","ROI.gtf"),peakcaller=PEAKCALLERS),
# counts matrix
expand(join(RESULTSDIR,"peaks","{peakcaller}","ROI.counts.tsv"),peakcaller=PEAKCALLERS),
# consensus peaks
expand(join(PEAKSDIR, "{peakcaller}", "fixed_width", "{sample}.{peakcaller}.renormalized.fixed_width.consensus.narrowPeak.annotated.gz"), peakcaller=PEAKCALLERS, sample=SAMPLES),
# spikein counts and scaling factors
expand(join(RESULTSDIR, "spikein", "{replicate}", "{replicate}.counts"), replicate=REPLICATES),
join(RESULTSDIR, "spikein", "scaling_factors.tsv"),
# expand(join(RESULTSDIR, "peaks", "{peakcaller}", "fixed_width", "counts", "ROI.{peakcaller}.{method}_scaled_counts.tsv"), method=COUNTING_METHODS, peakcaller=PEAKCALLERS),
expand(join(RESULTSDIR, "peaks", "{peakcaller}", "fixed_width", "counts", "ROI.{peakcaller}.{method}_scaled_counts.tsv"), method=COUNTING_METHODS, peakcaller=PEAKCALLERS),
# visualizations
expand(join(RESULTSDIR, "visualization", "{method}_bam", "{replicate}.{method}.bam"), method=COUNTING_METHODS, replicate=REPLICATES),
expand(join(RESULTSDIR, "visualization", "{method}_bigwig", "{replicate}.{method}.bw"), method=COUNTING_METHODS, replicate=REPLICATES),
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2 changes: 1 addition & 1 deletion workflow/rules/diffatac.smk
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Expand Up @@ -19,7 +19,7 @@ rule atac_calculate_regions_of_interest_for_diffatac:
# take genrich/macs consensus fixed width peaks and calculate ROIs
# """
input:
expand(join(RESULTSDIR,"peaks","{{peakcaller}}","fixed_width","{sample}.renormalized.fixed_width.consensus.narrowPeak"),sample=SAMPLES)
expand(join(RESULTSDIR,"peaks","{{peakcaller}}","fixed_width","{sample}.{{peakcaller}}.renormalized.fixed_width.consensus.narrowPeak"),sample=SAMPLES)
output:
roi = join(RESULTSDIR,"peaks","{peakcaller}","fixed_width","ROI.{peakcaller}.narrowPeak"),
roi_bed = join(RESULTSDIR,"peaks","{peakcaller}","fixed_width","ROI.{peakcaller}.bed"),
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