Snakemake does not give output files. Gives no errors

Question

[kamanovae]

Hi!

My cod looks like this:

import os

(SAMPLES,) = glob_wildcards("../exom/NIST7035/{sample}_L001_R1_001.fastq")
SAMPLE_PATH=os.path.dirname(config["sample"])

rule all:
        input:
                expand(config["out"] + "/{sample}/{sample}_R1.fastq", sample=SAMPLES),
                expand(config["out"] + "/{sample}/{sample}_R2.fastq", sample=SAMPLES)

rule sort:
        output:
                output1=config["out"] + "/{sample}/{sample}_R1.fastq", output2=config["out"] + "/{sample}/{sample}_R2.fastq"
        shell:
                " zcat  {SAMPLE_PATH}/{wildcards.sample}*R1*.fastq.gz | paste - - - - |  sort -k1,1 -S 30G | tr '\t' '\n' > {output.output1} ;"
                " zcat  {SAMPLE_PATH}/{wildcards.sample}*R2*.fastq.gz | paste - - - - |  sort -k1,1 -S 30G | tr '\t' '\n' > {output.output2}"

The snakemake terminates without output files without throwing an error

Building DAG of jobs...
Using shell: /bin/bash
Provided cores: 2
Rules claiming more threads will be scaled down.
Job stats:
job      count    min threads    max threads
-----  -------  -------------  -------------
all          1              1              1
total        1              1              1

Select jobs to execute...

[Thu Feb  3 12:43:46 2022]
localrule all:
    jobid: 0
    resources: tmpdir=/tmp

[Thu Feb  3 12:43:46 2022]
Finished job 0.
1 of 1 steps (100%) done
Complete log: /storage1/GatkBwaTest/SnakemakeDir/.snakemake/log/2022-02-03T124346.250486.snakemake.log

Maybe someone knows what I'm doing wrong? Thanks!

[cpad0112]

check if SAMPLES are listing files, check if ouptut directories and expected files already exist in output directories. There are few other issues with the code. As far as I know, this part of the code {wildcards.sample}*R1*.fastq.gz should fail with warning.