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Update Snakefile #2

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Update Snakefile #2

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8 changes: 5 additions & 3 deletions workflow/Snakefile
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Original file line number Diff line number Diff line change
Expand Up @@ -27,13 +27,15 @@ rule all:
rule minimap2_align:
input:
genome = genome_fasta,
fq = READSDIR / "{sample}"
fq = READSDIR + "/{sample}"
params:
outdir = OUTDIR,
opts = config["minimap2_opts"]
output:
sam_files = OUTDIR / "{sample}.sam"
sam_files = OUTDIR + "/{sample}.sam"
threads: 4
resources:
mem=10G
singularity:
'docker://quay.io/biocontainers/minimap2:2.17--h5bf99c6_4'
shell:
Expand All @@ -55,7 +57,7 @@ rule get_SJs_from_gtf:
params:
outdir = OUTDIR
output:
splicejns = OUTDIR / "spliceJns.txt"
splicejns = OUTDIR + "/spliceJns.txt"
threads: 1
singularity:
"docker://biocontainers/transcriptclean:v2.0.2_cv1"
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