I am trying to make a Snakemake pipeline using a configuration file config.yaml.

--- 
samples:
- Sample_1: reads/raw_reads_1
- Sample_2: reads/raw_reads_2
- Sample_3: reads/raw_reads_3

reference:
- "path/to/reference.fasta" 
...

Following the good practices given in the Snakemake wrapper repository, I have used wrappers commands as much as possible. https://snakemake-wrappers.readthedocs.io/en/stable/ However I have observed that the input/outputs of the different wrappers do not match. Is there a way to manage the names of the files between the rules to connect the wrappers without modifying them?

import os
import snakemake.io
import glob

configfile: "config.yaml"

rule all:
        input:
                expand("mapped/{sample}.bam", sample=config["samples"])

rule fastqc:
        input:
                "reads/{sample}.fastq"
        output:
                html="qc/fastqc/{sample}.html",
                zip="qc/fastqc/{sample}_fastqc.zip" # the suffix _fastqc.zip is necessary for multiqc to find the file. If not using multiqc, you are free to choose an arbitrary filename
        params:
                extra = "--quiet"
        log:
                "logs/fastqc/{sample}.log"
        threads: 1
        resources:
                mem_mb = 1024
        wrapper:
                "v2.6.0/bio/fastqc"

rule bwa_index:
        input:
                "{genome}.fasta", 
        output:
                idx=multiext("{genome}", ".amb", ".ann", ".bwt", ".pac", ".sa"),
        log:
                "logs/bwa_index/{genome}.log",
        params:
                algorithm="bwtsw",
        wrapper:
                "v2.6.0/bio/bwa/index"

rule bwa_mem:
        input:
                reads=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"],
                idx=multiext("genome", ".amb", ".ann", ".bwt", ".pac", ".sa"),
        output:
                "mapped/{sample}.bam",
        log:
                "logs/bwa_mem/{sample}.log",
        params:
                extra=r"-R '@RG\tID:{sample}\tSM:{sample}'",
                sorting="none",  # Can be 'none', 'samtools' or 'picard'.
                sort_order="queryname",  # Can be 'queryname' or 'coordinate'.
                sort_extra="",  # Extra args for samtools/picard.
                threads: 8
        wrapper:
                "v2.6.0/bio/bwa/mem"