title: rule not executing in snakemake workflow for read mapping with bwa, samtools
body: <p>Trying to set up a basic read mapping workflow.  The read mapping rule runs ok and makes a .sam file,  but snakemake skips the second rule that runs samtools fixmate on that .sam file to make a .bam file.</p>
  <pre><code>rule all:
      input:
          &quot;{sample}.bam&quot;
  
  
  rule bwa_map:
      params:
          index=&quot;../ref/GCF_000004255.2_v.1.0_genomic&quot;
      input:
          &quot;{sample}_1.fastq&quot;,
          &quot;{sample}_2.fastq&quot;
      output:
          &quot;{sample}.sam&quot;
      shell:
          &quot;bwa mem -M -t 6 -r 1 -o {output} {params.index} {input}&quot;
  
  rule fixmate:
          input:
                  &quot;{sample}.sam&quot;
          output:
                  &quot;{sample}.bam&quot;
          shell:
                  &quot;samtools fixmate -O bam {input} {output}&quot;
  </code></pre>