Snakemake specify a new wildcard in a new rule - wildcard

Question

I have input files:
Bob_1.fastq.gz
Bob_2.fastq.gz
Bob_3.fastq.gz
Bob_4.fastq.gz
Ron_1.fastq.gz
Ron_2.fastq.gz
Ron_3.fastq.gz
Ron_4.fastq.gz
I am running demultiplexing and trimming steps in one snakefile, like this:
workdir: "/path/to/dir/"
(SAMPLES,) =glob_wildcards('/path/to/dir/raw/{sample}.fastq.gz')
rule all:
input:
expand("demulptiplex/{sample}.fastq.gz", sample=SAMPLES),
expand("trimmed/{sample}.trimmed.fastq.gz", sample=SAMPLES)
rule sabre:
input:
infile="/path/to/dir/raw/{sample}.fastq.gz",
barcodefile= "files/{sample}.txt"
output:
unknownfile=temp("demulptiplex/unknown_barcode_{sample}.fastq.gz"),
shell:
"""
/Tools/sabre-master2/sabre se -f {input.infile} -b {input.barcodefile} -u {output.unknownfile}
"""
rule trimmomatic_se:
input:
r="{sample}.fastq.gz"
output:
r="trimmed/{sample}.trimmed.fastq.gz"
threads: 10
shell:
"""java -jar /Tools/Trimmomatic-0.36/trimmomatic-0.36.jar SE -threads {threads} {input.r} {output.r} ILLUMINACLIP:/Tools/Trimmomatic-0.36/adapters/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36"""
The demultiplex output files are like this:
Bob_1_CL1.fastq.gz.... Bob_1_CL345.fastq.gz
Bob_2_CL1.fastq.gz.... Bob_1_CL248.fastq.gz
Ron_1_dad1.fastq.gz... Ron_1_dad67.fastq.gz
and so on
So,if I do not specify the demultiplex output file the program would create it by itself. My problem is how to specify/introduce a new wildcard from the output of the previous rule in the next trimming step, as the wildcards are different from initial sample now.

Answer 1

Wildcards just need to be consistent in a rule, not across the workflow. The issue here is that you have a rule generating 'unknown' outputs that you need to process further. For that you need to use checkpoints.
Read through the second block of code about aggregating. Your checkpoint will be demultiplexing and if you don't have any other steps, all will be your aggregate step that calls checkpoints.demultiplex.get. If you search for checkpoint on stackoverflow you will find lots of examples; it's a hard feature to use at first!