bwa_mem.xml

<tool name="BWA_MEM_Alignment"
    threads="12"
    walltime="8:00:00"
    tool_config_prefix="bwa_mem_align">
    <description>
        First process a fastq file to extract read group information with
        read_group_from_fastq.py. Then align a pair of fastq files.
        Any quality checking and trimming must be done before this step.
    </description>
    <!-- Files:
        Ins:
          1: fastq_e1
          2: fastq_e2
          3: index prefix
          4: rg_info
        Outs:
          1: sam
    -->
    
    <!-- Modules needed to run on the cluster -->
    <module>bwakit/0.7.15</module>
    <module>samtools/0.1.18</module>
    <module>python/2.7.3</module>

    <!-- will be written to the default output dir -->
    <file id="read_group" temp="True" filespec="read_group.txt" />
    <!--
        Files:
        Ins: fastq
        Outs: read_group_data
    -->

    <!-- No special modules needed

     -->
    <command program="read_group_from_fastq.py">
      <version_command>read_group_from_fastq.py --version</version_command>
      {in_1} {read_group}
    </command>
    
    <!--
        Files we have to verify as unchanged, in addition to the commands.
        (Command program names are automatically added to the validate list,
        so they don't need to be added here. (Here, the reference sequence.)
    -->

   <file id="bwa7_idx_pfx" filespec="hs38DH.fa" in_dir="in_3" />

   <file id="bwa_alt" input="True"
        filespec="hg38_bwa_alt_aware_indices/bwa" />
   <file id="seqtk" input="True"
        filespec="hg38_bwa_alt_aware_indices/seqtk" />
   <file id="k8" input="True"
        filespec="hg38_bwa_alt_aware_indices/k8" />
   <file id="postalt" input="True"
        filespec="hg38_bwa_alt_aware_indices/bwa-postalt.js" />


 <file id="merged_fq" temp="True"
        filespec="merged.fastq" />
 <file id="intial_sam" temp="True"
        filespec="temp.sam" />
  <file id="out" temp="True"
        filespec="out" />

<file id="refalt" input="True"
        filespec="hg38_bwa_alt_aware_indices/hs38DH.fa.alt" />

<file id="samtools" input="True"
        filespec="hg38_bwa_alt_aware_indices/samtools" />




    <!--
        Create file entries for all the bwa index files purely for the
        ability to validate them. We actually just pass the index
        prefix into bwa; it knows about all the extensions.
    -->
    <file id="idx_1" in_dir="in_3" based_on="bwa7_idx_pfx"
          append=".amb" />
    <file id="idx_2" in_dir="in_3" based_on="bwa7_idx_pfx"
          append=".ann" />
    <file id="idx_3" in_dir="in_3" based_on="bwa7_idx_pfx"
          append=".bwt" />
    <file id="idx_4" in_dir="in_3" based_on="bwa7_idx_pfx"
          append=".pac" />
    <file id="idx_5" in_dir="in_3" based_on="bwa7_idx_pfx"
          append=".sa" />
    <validate id="idx_1" />
    <validate id="idx_2" />
    <validate id="idx_3" />
    <validate id="idx_4" />
    <validate id="idx_5" />

    <!-- Create an option for the read group, from the contents of rg_info -->
    <option name="rg" command_text="-R" from_file="read_group" />

    <option name="threads" command_text="-t" type="threads" />



    <command program="">
    hg38_bwa_alt_aware_indices/run-bwamem -t 12   {rg} -o out -H {bwa7_idx_pfx} {in_1} {in_2} | sh
    </command>
  

</tool>