Salmon indexing run for each trimmed fastq

[jimmybgammyknee]

Instead of indexing the transcriptome at the start of each code block, I have indexed a copy of mm10 on AFW. Can this be changed in the code?

i.e.
rule quant_salmon:
input:
R1 = config["BASE"] + config["TRIM"] + "/{samples}_t1.fastq.gz",
R2 = config["BASE"] + config["TRIM"] + "/{samples}_t2.fastq.gz",
Tran = config["TRAN"]
output:
out = config["BASE"] + config["QUANT_SAL"] + "/{samples}/"
params:
salmon = config["salmon"],
index = config["INDEX_DIR"],
bootstrap = config["bootstrap"],
out = config["BASE"] + config["QUANT_SAL"] + "/{samples}/"
threads: config["SAL_threads"]
message:
"Salmon - Quantification of transcripts"
log:
config["BASE"] + config["LOG"] + config["QUANT_SAL"] + "/{samples}.log"

shell:
 """
    {params.salmon} quant -l A -i **{params.index}** -p {threads} -1 {input.R1} -2 {input.R2} \
            --numBootstraps {params.bootstrap} -o {params.out} 2> {log}
 """

[a-lud]

Should be solved. I've included a new rule salmon_index, and it's output is directed to salmon_quant. The index step will only be executed once for the pipeline, and will occur before the quantification stage.

Let me know if there are any issues.