Snakemake problem: Merge all files together with space delimiter instead of iterating through it - snakemake

Question

I was trying to run a command which ideally looks like this,
minimap2 -a -x map-ont -t 20 /staging/reference.fasta fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample01.bam
Similarly, I have multiple samples (referring to fastq/sample01.fastq) in the folder.
The snakemake file I wrote to automate this behaviour is, however, parsing all files at once in the command like,
minimap2 -a -x map-ont -t 1 /staging/reference.fasta fastq/sample02.fastq fastq/sample03.fastq fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample02.bam fastq_minon/sample03.bam fastq_minon/sample01.bam
I have pasted the code and logs below. Please help me try to figure out this mistake.
Code
SAMPLES, = glob_wildcards("fastq/{smp}.fastq")
rule minimap:
input:
expand("fastq/{smp}.fastq", smp=SAMPLES)
output:
expand("fastq_minon/{smp}.bam", smp=SAMPLES)
params:
ref = FASTA
threads: 40
shell:
"""
minimap2 -a -x map-ont -t {threads} {params.ref} {input} | samtools view -bS -F 4 - | samtools sort -o {output}
"""
log
Building DAG of jobs...
Job counts:
count jobs
1 minimap
1
[Tue May 5 03:28:50 2020]
rule minimap:
input: fastq/sample02.fastq, fastq/sample03.fastq, fastq/sample01.fastq
output: fastq_minon/sample02.bam, fastq_minon/sample03.bam, fastq_minon/sample01.bam
jobid: 0
minimap2 -a -x map-ont -t 1 /staging/reference.fasta fastq/sample02.fastq fastq/sample03.fastq fastq/sample01.fastq | samtools view -bS -F 4 - | samtools sort -o fastq_minon/sample02.bam fastq_minon/sample03.bam fastq_minon/sample01.bam
Job counts:
count jobs
1 minimap
1
This was a dry-run (flag -n). The order of jobs does not reflect the order of execution.

Answer 1

The expand function is used to create a list. Thus, in your rule minimap, you're telling snakemake that you want all fastq files as input and that the rule will produce as many bam files. What you want is a rule that will be triggered for every sample using a wildcard:
SAMPLES, = glob_wildcards("fastq/{smp}.fastq")
rule all:
input: expand("fastq_minon/{smp}.bam", smp=SAMPLES)
rule minimap:
input:
"fastq/{smp}.fastq"
output:
"fastq_minon/{smp}.bam"
params:
ref = FASTA
threads: 40
shell:
"""
minimap2 -a -x map-ont -t {threads} {params.ref} {input} | samtools view -bS -F 4 - | samtools sort -o {output}
"""
By defining all the files wanted in rule all, the rule minimap will be triggered as many times as necessary to create ONE bam file from ONE fastq file.
Have a look at my answer to this question to understand the use of wildcards and expand.