From 43289bb947f960a870f091597a55919714ad5650 Mon Sep 17 00:00:00 2001 From: Austin Gillen Date: Tue, 30 Jan 2024 11:20:57 -0700 Subject: [PATCH] fix naming in Snakefile to make less awkward --- Snakefile | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/Snakefile b/Snakefile index 1312668..fb9e163 100644 --- a/Snakefile +++ b/Snakefile @@ -21,11 +21,11 @@ with open('chemistry.json') as fp: chemistry = json.load(fp) # paired positional approach -PAIREDs = [] +PAIRs = [] if PAIRED_SAMPLES: - PAIREDs.extend(expand("{results}/counts/{sample}_{read}_counts.tsv.gz", results = RESULTS, sample = PAIRED_SAMPLES, read = "paired")) - PAIREDs.extend(expand("{results}/{sample}/{sample}_{read}_Aligned.sortedByCoord.out.bam", results = RESULTS, sample = PAIRED_SAMPLES, read = "paired")) - PAIREDs.extend(expand("{results}/bed/{sample}_{read}.bed.gz", results = RESULTS, sample = PAIRED_SAMPLES, read = "paired")) + PAIRs.extend(expand("{results}/counts/{sample}_{read}_counts.tsv.gz", results = RESULTS, sample = PAIRED_SAMPLES, read = "paired")) + PAIRs.extend(expand("{results}/{sample}/{sample}_{read}_Aligned.sortedByCoord.out.bam", results = RESULTS, sample = PAIRED_SAMPLES, read = "paired")) + PAIRs.extend(expand("{results}/bed/{sample}_{read}.bed.gz", results = RESULTS, sample = PAIRED_SAMPLES, read = "paired")) # read 1 positional approach R1s = [] if R1_SAMPLES: @@ -39,7 +39,7 @@ if R2_SAMPLES: R2s.extend(expand("{results}/{sample}/{sample}_{read}_Aligned.sortedByCoord.out.bam", results = RESULTS, sample = R2_SAMPLES, read = "R2")) R2s.extend(expand("{results}/bed/{sample}_{read}.bed.gz", results = RESULTS, sample = R2_SAMPLES, read = "R2")) # combine -all_outputs = PAIREDs + R1s + R2s #+ expand("{results}/report/multiqc_report.html", results = RESULTS) +all_outputs = PAIRs + R1s + R2s #+ expand("{results}/report/multiqc_report.html", results = RESULTS) print(all_outputs) rule all: