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my Salmon Snakemake file
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| scratch <- "/pine/scr/m/i/milove" | |
| # see https://gist.github.com/mikelove/f539631f9e187a8931d34779436a1c01 for accession2url() definition | |
| source("https://gist.github.com/mikelove/f539631f9e187a8931d34779436a1c01/raw/6e6633aa5123358b70390ab738be1eef03a3df31/accession2url.R") | |
| for (i in 1:nrow(x)) { | |
| print(paste("---",i,"---")) | |
| run <- x$Run[i] | |
| for (read in 1:2) { | |
| file <- paste0(run,"_",read,".fastq.gz") | |
| url <- file.path(accession2url(run), file) | |
| dest <- file.path(scratch, file) | |
| if (!file.exists(dest)) | |
| download.file(url, dest) | |
| } | |
| } |
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| #!/bin/bash | |
| # | |
| #SBATCH --job-name=snake | |
| #SBATCH --time=240 | |
| #SBATCH --mem=1000 | |
| module load python | |
| snakemake -j 4 --latency-wait 30 --cluster "sbatch -n 8 -N 1 --mem=10000 --time 60" |
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| RUNS, = glob_wildcards("/pine/scr/m/i/milove/{run}_1.fastq.gz") | |
| SALMON = "/proj/milovelab/bin/salmon-1.3.0_linux_x86_64/bin/salmon" | |
| ANNO = "/proj/milovelab/anno" | |
| rule all: | |
| input: expand("quants/{run}/quant.sf", run=RUNS) | |
| rule salmon_index: | |
| input: "{ANNO}/gencode.vXYZ.transcripts.fa.gz" | |
| output: directory("{ANNO}/gencode.vXYZ-salmon_1.3.0") | |
| shell: "{SALMON} index --gencode -p 8 -t {input} -i {output}" | |
| rule salmon_quant: | |
| input: | |
| r1 = "/pine/scr/m/i/milove/{sample}_1.fastq.gz", | |
| r2 = "/pine/scr/m/i/milove/{sample}_2.fastq.gz", | |
| index = "/proj/milovelab/anno/gencode.vXYZ-salmon_1.3.0" | |
| output: | |
| "quants/{sample}/quant.sf" | |
| params: | |
| dir = "quants/{sample}" | |
| shell: | |
| "{SALMON} quant -i {input.index} -l A -p 8 --gcBias " | |
| "--numGibbsSamples 30 --thinningFactor 100 " | |
| "-o {params.dir} -1 {input.r1} -2 {input.r2}" |
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