WorkflowError in file /home/ubuntu/snaketest/Snakefile, line 28:
Flags ({'storage_object': <snakemake_storage_plugin_fs.StorageObject object at 0x7ebd211710a0>}) in file pattern '.snakemake/storage/fs/home/ubuntu/data/sorted_reads/{sample}.bam' given to expand() are invalid. Flags (e.g. temp(), directory()) have to be applied outside of expand (e.g. 'temp(expand("plots/{sample}.pdf", sample=SAMPLES))').

SAMPLES=["A", "B"]

rule all:
    input:
        "calls/all.vcf"

rule bwa_map:
    input:
        "data/genome.fa",
        "data/samples/{sample}.fastq"
    output:
        "mapped_reads/{sample}.bam"
    shell:
        "bwa mem {input} | samtools view -Sb - > {output}"

rule samtools_sort:
    input:
        "mapped_reads/{sample}.bam"
    output:
        "sorted_reads/{sample}.bam"
    shell:
        "samtools sort -T sorted_reads/{wildcards.sample} "
        "-O bam {input} > {output}"

rule bcftools_call:
    input:
        fa="data/genome.fa",
        bam=collect(rules.samtools_sort.output, sample=SAMPLES)
    output:
        "calls/all.vcf"
    shell:
        "bcftools mpileup -f {input.fa} {input.bam} | "
        "bcftools call -mv - > {output}"