Snakemake: Exchanging variables - snakemake

Question

I have some ONT sequencing runs that have been basecalled on the MINIT. As such, when I demultiplex with guppy_barcoder, I get a directory of fastq files for each barcode. I want to use snakemake as a workflow manager to take these fastq files through our analyses, but this involves swapping the {barcode} for {sample} at some point.
BARCODE=['barcode01', 'barcode02', 'barcode03', 'barcode04']
SAMPLE=['sample01', 'sample02', 'sample03', 'sample04']
rule all:
input:
directory(expand("Sequencing_reads/demultiplexed/{barcode}", barcode=BARCODE)), #guppy_barcoder
expand("Sequencing_reads/gathered/{sample}_ONT.fastq", sample=SAMPLE), #getting all of the fastq files with the same barcode assigned to the correct sample
rule demultiplex:
input:
glob.glob("Sequencing_reads/fastq_pass/*fastq")
output:
directory(expand("Sequencing_reads/demultiplexed/{barcode}", barcode=BARCODE))
shell:
"guppy_barcoder --input_path Sequencing_reads/fastq_pass --save_path Sequencing_reads/demultiplexed -r "
rule gather:
input:
rules.demultiplex.output
output:
"Sequencing_reads/gathered/{sample}_ONT.fastq"
shell:
"cat Sequencing_reads/demultiplexed/{wildcards.barcode}/*fastq > {output.fastq} "
This does give me an error:
RuleException in line 32 of /home/eriny/sandbox/ONT_unicycler_pipeline/ONT_pipeline.smk:
'Wildcards' object has no attribute 'barcode'
But I actually think I'm missing something conceptually. I would like rule gather to be something like:
cat Sequencing_reads/demultiplexed/barcode01/*fastq > Sequencing_reads/gathered/sample01_ONT.fastq
I have tried setting up some dictionaries so that sample and barcode are given the same key, but my syntax must be broken.
I'm hoping to find a 1:1 way to map one variable name onto another.

Answer 1

I'm hoping to find a 1:1 way to map one variable name onto another.
I think the sample to dictionary is a possibility combined with a lambda as input function to get the barcode assign to a sample. For example:
BARCODE=['barcode01', 'barcode02', 'barcode03', 'barcode04']
SAMPLE=['sample01', 'sample02', 'sample03', 'sample04']
sam2bar= dict(zip(SAMPLE, BARCODE))
rule all:
input:
expand("Sequencing_reads/gathered/{sample}_ONT.fastq", sample=SAMPLE), #getting all of the fastq files with the same barcode assigned to the correct sample
rule demultiplex:
input:
glob.glob("Sequencing_reads/fastq_pass/*fastq"),
output:
done= touch('demux.done'), # This signals that guppy has completed
shell:
"guppy_barcoder --input_path Sequencing_reads/fastq_pass --save_path Sequencing_reads/demultiplexed -r "
rule gather:
input:
done= 'demux.done',
fastq= lambda wc: glob.glob("Sequencing_reads/demultiplexed/%s/*fastq" % sam2bar[wc.sample])
output:
fastq= "Sequencing_reads/gathered/{sample}_ONT.fastq"
shell:
"cat {input.fastq} > {output.fastq} "