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/seqware-webservice/src/test/resources/net/sourceforge/seqware/common/metadata/GATKRecalibrationAndVariantCalling_1.3.16.ftl

https://github.com/lazycrazyowl/seqware
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Possible License(s): GPL-3.0

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  1. <?xml version="1.0" encoding="UTF-8"?>
    2. 

  2. <adag xmlns="http://pegasus.isi.edu/schema/DAX" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://pegasus.isi.edu/schema/DAX http://pegasus.isi.edu/schema/dax-3.2.xsd" version="3.2" count="1" index="0" name="GATKRecalibrationAndVariantCalling_1.3.16">
    3. 

  3. 

  4. <#--
    5. 

  5. DESCRIPTION:
    6. 

  6. 

  7. This workflow is designed to take a BAM file, break it down by chromosome, perform realignment, recalibration,
    8. 

  8. duplicate flagging, and variant calling for small indels and SNVs. The result is a VCF file for SNVs and indels both filtered
    9. 

  9. and un-filtered.
    10. 

  10. 

  11. This workflow is designed to work with GATK version 1.3.16.
    12. 

  12. 

  13. Docs: 
    14. 

  14. 

  15. * http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v2
    16. 

  16. * http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit
    17. 

  17. 

  18. TODO: 
    19. 

  19. 

  20. * need to add WGS support where needed, see ./postProcessing/gatk/oicr_gatk_helper.sh
    21. 

  21. * need to add annotation steps?
    22. 

  22. -->
    23. 

  23. 

  24. <!-- the relative path -->
    25. 

  25. <#assign workflow_name = "GATKRecalibrationAndVariantCalling/1.x.x"/>
    26. 

  26. 

  27. <!-- MACRO: to create a mkdir pre job and stage mkdir binary -->
    28. 

  28. <#macro requires_dir dir>
    29. 

  29.   <profile namespace="env" key="GRIDSTART_PREJOB">/${workflow_bundle_dir}/${workflow_name}/bin/pegasus-dirmanager -c -d ${dir}</profile>
    30. 

  30. </#macro>
    31. 

  31. 

  32. <!-- VARS -->
    33. 

  33. <#-- Set seqware version -->
    34. 

  34. <#assign seqware_version = "0.10.0"/>
    35. 

  35. <#assign workflow_version = "1.3.16"/>
    36. 

  36. <#assign inputs="${bam_inputs}"/>
    37. 

  37. <#-- Set relative paths for files within the run-->
    38. 

  38. <#assign bin_dir = "bin"/>
    39. 

  39. <#assign data_dir = "data"/>
    40. 

  40. <#assign accession_dir = "accessions"/>
    41. 

  41. <#assign tmp_dir = "tmp"/>
    42. 

  42. <!-- parent accessions -->
    43. 

  43. <#assign parentAccessions = "${parent_accession}"/>
    44. 

  44. 

  45. <!-- EXECUTABLES INCLUDED WITH BUNDLE -->
    46. 

  46. <executable namespace="seqware" name="runner" version="${seqware_version}" 
    47. 

  47.             arch="x86_64" os="linux" installed="true" >
    48. 

  48.   <!-- the path to the tool that actually runs a given module -->
    49. 

  49.   <pfn url="file:///${workflow_bundle_dir}/${workflow_name}/bin/seqware-java-wrapper.sh" site="${seqware_cluster}"/>
    50. 

  50. </executable>
    51. 

  51. 

  52. <executable namespace="pegasus" name="dirmanager" version="${seqware_version}" 
    53. 

  53.             arch="x86_64" os="linux" installed="true" >
    54. 

  54.   <!-- the path to the tool that creates directories -->
    55. 

  55.   <pfn url="file:///${workflow_bundle_dir}/${workflow_name}/bin/pegasus-dirmanager" site="${seqware_cluster}"/>
    56. 

  56. </executable>
    57. 

  57. 

  58. 

  59. 

  60. <!-- PROVISION -->
    61. 

  61. 

  62. <!-- Part 1: Job definitions -->
    63. 

  63. 

  64.   <!-- Pre Job: make directories -->
    65. 

  65.   <job id="IDPRE0.1" namespace="pegasus" name="dirmanager" version="${seqware_version}">
    66. 

  66.     <argument>
    67. 

  67.       -c -d ${bin_dir}
    68. 

  68.     </argument>
    69. 

  69.     <profile namespace="globus" key="jobtype">condor</profile>
    70. 

  70.     <profile namespace="globus" key="count">1</profile>
    71. 

  71.     <profile namespace="globus" key="maxmemory">500</profile>
    72. 

  72.   </job>
    73. 

  73. 

  74.   <!-- Pre Job: make directories -->
    75. 

  75.   <job id="IDPRE0.2" namespace="pegasus" name="dirmanager" version="${seqware_version}">
    76. 

  76.     <argument>
    77. 

  77.       -c -d ${data_dir}
    78. 

  78.     </argument>
    79. 

  79.     <profile namespace="globus" key="jobtype">condor</profile>
    80. 

  80.     <profile namespace="globus" key="count">1</profile>
    81. 

  81.     <profile namespace="globus" key="maxmemory">500</profile>
    82. 

  82.   </job>
    83. 

  83. 

  84.   <!-- Pre Job: make directories -->
    85. 

  85.   <job id="IDPRE0.3" namespace="pegasus" name="dirmanager" version="${seqware_version}">
    86. 

  86.     <argument>
    87. 

  87.       -c -d ${accession_dir}
    88. 

  88.     </argument>
    89. 

  89.     <profile namespace="globus" key="jobtype">condor</profile>
    90. 

  90.     <profile namespace="globus" key="count">1</profile>
    91. 

  91.     <profile namespace="globus" key="maxmemory">500</profile>
    92. 

  92.   </job>
    93. 

  93. 

  94.   <!-- Pre Job: make directories -->
    95. 

  95.   <job id="IDPRE0.4" namespace="pegasus" name="dirmanager" version="${seqware_version}">
    96. 

  96.     <argument>
    97. 

  97.       -c -d ${tmp_dir}
    98. 

  98.     </argument>
    99. 

  99.     <profile namespace="globus" key="jobtype">condor</profile>
    100. 

  100.     <profile namespace="globus" key="count">1</profile>
    101. 

  101.     <profile namespace="globus" key="maxmemory">500</profile>
    102. 

  102.   </job>
    103. 

  103. 

  104.   <!-- Jobs for making data and scripts available -->
    105. 

  105. 

  106.   <!-- Pre Job: makes seqware perl scripts available -->
    107. 

  107.   <job id="IDPRE1" namespace="seqware" name="runner" version="${seqware_version}">
    108. 

  108.     <argument>
    109. 

  109.       -Xmx1000M
    110. 

  110.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    111. 

  111.       net.sourceforge.seqware.pipeline.runner.Runner
    112. 

  112.       --no-metadata
    113. 

  113.       --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
    114. 

  114.       --
    115. 

  115.       --input-file ${workflow_bundle_dir}/${workflow_name}/dependencies/noarch/seqware-pipeline-perl-bin.noarch.zip
    116. 

  116.       --output-dir ${bin_dir}
    117. 

  117.     </argument>
    118. 

  118. 

  119.     <profile namespace="globus" key="jobtype">condor</profile>
    120. 

  120.     <profile namespace="globus" key="count">1</profile>
    121. 

  121.     <profile namespace="globus" key="maxmemory">2000</profile>
    122. 

  122. 

  123.   </job>
    124. 

  124. 

  125.   <!-- Pre Job: makes annovar scripts available-->
    126. 

  126.   <job id="IDPRE2" namespace="seqware" name="runner" version="${seqware_version}">
    127. 

  127.     <argument>
    128. 

  128.       -Xmx1000M
    129. 

  129.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    130. 

  130.       net.sourceforge.seqware.pipeline.runner.Runner
    131. 

  131.       --no-metadata
    132. 

  132.       --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
    133. 

  133.       --
    134. 

  134.       --input-file ${workflow_bundle_dir}/${workflow_name}/dependencies/noarch/annovar-20110506.noarch.zip
    135. 

  135.       --output-dir ${bin_dir}
    136. 

  136.     </argument>
    137. 

  137. 

  138.     <profile namespace="globus" key="jobtype">condor</profile>
    139. 

  139.     <profile namespace="globus" key="count">1</profile>
    140. 

  140.     <profile namespace="globus" key="maxmemory">2000</profile>
    141. 

  141. 

  142.   </job>
    143. 

  143. 

  144. <!-- TODO: Update to latest version -->
    145. 

  145. 

  146.   <!-- Pre Job: makes GATK available -->
    147. 

  147.   <job id="IDPRE3" namespace="seqware" name="runner" version="${seqware_version}">
    148. 

  148.     <argument>
    149. 

  149.       -Xmx1000M
    150. 

  150.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    151. 

  151.       net.sourceforge.seqware.pipeline.runner.Runner
    152. 

  152.       --no-metadata
    153. 

  153.       --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
    154. 

  154.       --
    155. 

  155.       --input-file ${workflow_bundle_dir}/${workflow_name}/dependencies/noarch/GenomeAnalysisTK-1.3.16.g6a5d5e7.noarch.zip
    156. 

  156.       --output-dir ${bin_dir}
    157. 

  157.     </argument>
    158. 

  158. 

  159.     <profile namespace="globus" key="jobtype">condor</profile>
    160. 

  160.     <profile namespace="globus" key="count">1</profile>
    161. 

  161.     <profile namespace="globus" key="maxmemory">2000</profile>
    162. 

  162. 

  163.   </job>
    164. 

  164. 

  165.   <!-- Pre Job: makes picard available -->
    166. 

  166.   <job id="IDPRE4" namespace="seqware" name="runner" version="${seqware_version}">
    167. 

  167.     <argument>
    168. 

  168.       -Xmx1000M
    169. 

  169.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    170. 

  170.       net.sourceforge.seqware.pipeline.runner.Runner
    171. 

  171.       --no-metadata
    172. 

  172.       --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
    173. 

  173.       --
    174. 

  174.       --input-file ${workflow_bundle_dir}/${workflow_name}/dependencies/noarch/picard-tools-1.48.noarch.zip
    175. 

  175.       --output-dir ${bin_dir}
    176. 

  176.     </argument>
    177. 

  177. 

  178.     <profile namespace="globus" key="jobtype">condor</profile>
    179. 

  179.     <profile namespace="globus" key="count">1</profile>
    180. 

  180.     <profile namespace="globus" key="maxmemory">2000</profile>
    181. 

  181. 

  182.   </job>
    183. 

  183. 

  184.   <!-- Pre Job: makes samtools available -->
    185. 

  185.   <job id="IDPRE5" namespace="seqware" name="runner" version="${seqware_version}">
    186. 

  186.     <argument>
    187. 

  187.       -Xmx1000M
    188. 

  188.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    189. 

  189.       net.sourceforge.seqware.pipeline.runner.Runner
    190. 

  190.       --no-metadata
    191. 

  191.       --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionDependenciesBundle
    192. 

  192.       --
    193. 

  193.       --input-file ${workflow_bundle_dir}/${workflow_name}/dependencies/x86_64/samtools-0.1.17.x86_64.zip
    194. 

  194.       --output-dir ${bin_dir}
    195. 

  195.     </argument>
    196. 

  196. 

  197.     <profile namespace="globus" key="jobtype">condor</profile>
    198. 

  198.     <profile namespace="globus" key="count">1</profile>
    199. 

  199.     <profile namespace="globus" key="maxmemory">2000</profile>
    200. 

  200. 

  201.   </job>
    202. 

  202. 

  203. 

  204. <!-- MODULE CALLS -->
    205. 

  205. 

  206. <!-- 
    207. 

  207. Overview: 
    208. 

  208. 

  209. * want to do a merge of all the Bam files and then do target and realignment
    210. 

  210. * realign per chr
    211. 

  211. * then merge everything
    212. 

  212. * collapse at that point
    213. 

  213. -->
    214. 

  214. 

  215. <!-- BEGIN LOOP: provision input BAM files and then index them -->
    216. 

  216. <#list inputs?split(",") as input>
    217. 

  217. 

  218.   <#list input?split("/") as tmp>
    219. 

  219.     <#assign basename = tmp/>
    220. 

  220.   </#list>
    221. 

  221. 

  222.   <!-- Job: figure out if the input is a URL and, if it is, correclty download it to a staging area otherwise link to it -->
    223. 

  223.   <job id="ID0.${input_index}" namespace="seqware" name="runner" version="${seqware_version}">
    224. 

  224.     <argument>
    225. 

  225.       -Xmx1000M
    226. 

  226.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    227. 

  227.       net.sourceforge.seqware.pipeline.runner.Runner
    228. 

  228.       --no-metadata
    229. 

  229.       --module net.sourceforge.seqware.pipeline.modules.utilities.ProvisionFiles
    230. 

  230.       --
    231. 

  231.       --input-file ${input}
    232. 

  232.       --output-dir ${data_dir}
    233. 

  233.     </argument>
    234. 

  234. 

  235.     <profile namespace="globus" key="jobtype">condor</profile>
    236. 

  236.     <profile namespace="globus" key="count">1</profile>
    237. 

  237.     <profile namespace="globus" key="maxmemory">2000</profile>
    238. 

  238. 

  239.   </job>
    240. 

  240. 

  241.   <!-- TODO: this needs to output in name sorted for the fixmate step, need to test -->
    242. 

  242.   <!-- Here's an example filtering based on quality too: samtools view -b -F 4 ./bam/110316_I580_00038_612RG_LT_s_1_sequence_SE_novoalign.sam.sorted.bam | samtools view -b -F 256 - | samtools view -b -q 30 - > tmp/110316_I580_00038_612RG_LT_s_1_sequence_SE_novoalign.sam.sorted.bam -->
    243. 

  243.   <!-- Job: Samtools filter out unmapped and multi-hit -->
    244. 

  244.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    245. 

  245.   <#assign algo = "SamtoolsUniqueHitFilter"/>
    246. 

  246.   <job id="ID1.${input_index}" namespace="seqware" name="runner" version="${seqware_version}">
    247. 

  247.     <argument>
    248. 

  248.       -Xmx1000M
    249. 

  249.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    250. 

  250.       net.sourceforge.seqware.pipeline.runner.Runner
    251. 

  251.       --${metadata}
    252. 

  252.       <#list parentAccessions?split(",") as pa>
    253. 

  253.       --metadata-parent-accession ${pa}
    254. 

  254.       </#list>
    255. 

  255.       --metadata-processing-accession-file ${accession_dir}/${algo}_${input_index}_accession
    256. 

  256.       --metadata-output-file-prefix ${output_prefix}
    257. 

  257.       --metadata-workflow-run-accession ${workflow_run_accession}
    258. 

  258.       --module ${module}
    259. 

  259.       --
    260. 

  260.       --gcr-algorithm ${algo}
    261. 

  261.       --gcr-command ${bin_dir}/${samtools} view -b -F 4 ${data_dir}/${basename} | ${bin_dir}/${samtools} view -b -F 256 - | ${bin_dir}/${samtools} sort -n -m ${samtools_slots_memory_gigabytes - 2}000000000 - ${data_dir}/${basename}.filtered.namesorted
    262. 

  262.     </argument>
    263. 

  263. 

  264.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    265. 

  265.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    266. 

  266.     <profile namespace="globus" key="jobtype">condor</profile>
    267. 

  267.     <profile namespace="globus" key="count">${samtools_slots}</profile>
    268. 

  268.     <profile namespace="globus" key="maxmemory">${samtools_slots_memory_gigabytes}000</profile>
    269. 

  269. 

  270.   </job>
    271. 

  271. 

  272.   <!-- Job: FixMateInfo -->
    273. 

  273.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    274. 

  274.   <#assign parentAlgo = "${algo}"/>
    275. 

  275.   <#assign algo = "PicardFixMateInformation"/>
    276. 

  276.   <job id="ID10.${input_index}" namespace="seqware" name="runner" version="${seqware_version}">
    277. 

  277.     <argument>
    278. 

  278.       -Xmx1000M
    279. 

  279.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    280. 

  280.       net.sourceforge.seqware.pipeline.runner.Runner
    281. 

  281.       --${metadata}
    282. 

  282.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${input_index}_accession
    283. 

  283.       --metadata-processing-accession-file ${accession_dir}/${algo}_${input_index}_accession
    284. 

  284.       --metadata-output-file-prefix ${output_prefix}
    285. 

  285.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    286. 

  286.       --module ${module}
    287. 

  287.       --
    288. 

  288.       --gcr-algorithm ${algo}
    289. 

  289.       --gcr-command ${java}
    290. 

  290.       -Xmx${picard_fixmate_mem}g
    291. 

  291.       -jar ${bin_dir}/${picardfixmate}
    292. 

  292.       INPUT=${data_dir}/${basename}.filtered.namesorted.bam
    293. 

  293.       OUTPUT=${data_dir}/${basename}.filtered.fixmate.sorted.bam
    294. 

  294.       VALIDATION_STRINGENCY=SILENT TMP_DIR=${tmp_dir}
    295. 

  295.       SORT_ORDER=coordinate
    296. 

  296.     </argument>
    297. 

  297. 

  298.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    299. 

  299.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    300. 

  300.     <profile namespace="globus" key="jobtype">condor</profile>
    301. 

  301.     <profile namespace="globus" key="count">${picard_slots}</profile>
    302. 

  302.     <profile namespace="globus" key="maxmemory">${picard_fixmate_mem + 4}000</profile>
    303. 

  303. 

  304.   </job>
    305. 

  305. 

  306.   <!-- Index input BAMs -->
    307. 

  307.   <#assign algo = "IndexBam1"/>
    308. 

  308.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    309. 

  309.   <job id="ID15.${input_index}" namespace="seqware" name="runner" version="${seqware_version}">
    310. 

  310.     <argument>
    311. 

  311.       -Xmx1000M
    312. 

  312.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    313. 

  313.       net.sourceforge.seqware.pipeline.runner.Runner
    314. 

  314.       --${metadata}
    315. 

  315.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${input_index}_accession
    316. 

  316.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    317. 

  317.       --metadata-output-file-prefix ${output_prefix}
    318. 

  318.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    319. 

  319.       --module ${module}
    320. 

  320.       --
    321. 

  321.       --gcr-algorithm ${algo}
    322. 

  322.       --gcr-command ${java}
    323. 

  323.       -Xmx${picard_index_bam_mem}g
    324. 

  324.       -jar ${bin_dir}/${picardindex}
    325. 

  325.       INPUT=${data_dir}/${basename}.filtered.fixmate.sorted.bam
    326. 

  326.     </argument>
    327. 

  327. 

  328.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    329. 

  329.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    330. 

  330.     <profile namespace="globus" key="jobtype">condor</profile>
    331. 

  331.     <profile namespace="globus" key="count">${picard_slots}</profile>
    332. 

  332.     <profile namespace="globus" key="maxmemory">${picard_index_bam_mem + 4}000</profile>
    333. 

  333. 

  334.   </job>
    335. 

  335. 

  336. </#list>
    337. 

  337. <!-- END LOOP: provision input BAM files and then index them -->
    338. 

  338. 

  339. 

  340. <!-- BEGIN LOOP: by chromosome -->
    341. 

  341. <#list chr_sizes?split(",") as chr_size>
    342. 

  342. 

  343.   <#assign chrArr = chr_size?split(":")/>
    344. 

  344.   <#assign chr = chrArr[0]/>
    345. 

  345.   <#assign size = chrArr[1]?number/>
    346. 

  346. 

  347.   <!-- Job: RealignerTargetCreator -->
    348. 

  348.   <#assign parentAlgo = "IndexBam1"/>
    349. 

  349.   <#assign algo = "RealignerTargetCreator"/>
    350. 

  350.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    351. 

  351.   <job id="ID20.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    352. 

  352.     <argument>
    353. 

  353.       -Xmx1000M
    354. 

  354.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    355. 

  355.       net.sourceforge.seqware.pipeline.runner.Runner
    356. 

  356.       --${metadata}
    357. 

  357.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_accession
    358. 

  358.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    359. 

  359.       --metadata-output-file-prefix ${output_prefix}
    360. 

  360.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    361. 

  361.       --module ${module}
    362. 

  362.       --
    363. 

  363.       --gcr-algorithm ${algo}
    364. 

  364.       --gcr-command ${java}
    365. 

  365.       -Xmx${gatk_realign_target_creator_mem}g
    366. 

  366.       -Djava.io.tmpdir=${tmp_dir} 
    367. 

  367.       -jar ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    368. 

  368.       -T RealignerTargetCreator
    369. 

  369.       -R ${ref_fasta}
    370. 

  370.       -o ${data_dir}/gatk.${chr}.intervals -L ${chr} -known ${gatk_dbsnp_vcf} -et NO_ET  
    371. 

  371. <#list inputs?split(",") as input>
    372. 

  372.   <#-- Set the basename from input name -->
    373. 

  373.   <#list input?split("/") as tmp>
    374. 

  374.     <#assign basename = tmp/>
    375. 

  375.   </#list>
    376. 

  376.       -I ${data_dir}/${basename}.filtered.fixmate.sorted.bam
    377. 

  377. </#list>
    378. 

  378.     </argument>
    379. 

  379. 

  380.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    381. 

  381.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    382. 

  382.     <profile namespace="globus" key="jobtype">condor</profile>
    383. 

  383.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    384. 

  384.     <profile namespace="globus" key="maxmemory">${gatk_indel_realigner_mem + 4}000</profile>
    385. 

  385. 

  386.   </job>
    387. 

  387. 

  388.   <!-- Job: IndelRealigner -->
    389. 

  389.   <!-- NOTE: I had to remove -targetNotSorted to get this to work -->
    390. 

  390.   <#assign parentAlgo = "RealignerTargetCreator"/>
    391. 

  391.   <#assign algo = "IndelRealigner"/>
    392. 

  392.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    393. 

  393.   <job id="ID30.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    394. 

  394.     <argument>
    395. 

  395.       -Xmx1000M
    396. 

  396.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    397. 

  397.       net.sourceforge.seqware.pipeline.runner.Runner
    398. 

  398.       --${metadata}
    399. 

  399.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    400. 

  400.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    401. 

  401.       --metadata-output-file-prefix ${output_prefix}
    402. 

  402.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    403. 

  403.       --module ${module}
    404. 

  404.       --
    405. 

  405.       --gcr-algorithm ${algo}
    406. 

  406.       --gcr-command ${java}
    407. 

  407.       -Xmx${gatk_indel_realigner_mem}g
    408. 

  408.       -Djava.io.tmpdir=${tmp_dir} 
    409. 

  409.       -jar ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    410. 

  410.       -R ${ref_fasta}
    411. 

  411.       -T IndelRealigner
    412. 

  412.       -L ${chr}
    413. 

  413.       -targetIntervals ${data_dir}/gatk.${chr}.intervals
    414. 

  414.       -o ${data_dir}/gatk.realigned.${chr}.bam
    415. 

  415.       -compress 0
    416. 

  416.       -et NO_ET
    417. 

  417. <#list inputs?split(",") as input>
    418. 

  418.   <#-- Set the basename from input name, removing .input -->
    419. 

  419.   <#list input?split("/") as tmp>
    420. 

  420.     <#assign basename = tmp/>
    421. 

  421.   </#list>
    422. 

  422.       -I ${data_dir}/${basename}.filtered.fixmate.sorted.bam
    423. 

  423. </#list>
    424. 

  424.     </argument>
    425. 

  425. 

  426.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    427. 

  427.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    428. 

  428.     <profile namespace="globus" key="jobtype">condor</profile>
    429. 

  429.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    430. 

  430.     <profile namespace="globus" key="maxmemory">${gatk_indel_realigner_mem + 4}000</profile>
    431. 

  431. 

  432.   </job>
    433. 

  433. 

  434.   <!-- Job: Sort by Query Name for Fixmate step, this require query name sort not coordinate, see http://picard.svn.sourceforge.net/viewvc/picard/tags/1.48/src/java/net/sf/picard/sam/FixMateInformation.java?revision=1005&view=markup -->
    435. 

  435.   <#assign parentAlgo = "IndelRealigner"/>
    436. 

  436.   <#assign algo = "RealignedBAMResorting"/>
    437. 

  437.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    438. 

  438.   <job id="ID35.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    439. 

  439.     <argument>
    440. 

  440.       -Xmx1000M
    441. 

  441.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    442. 

  442.       net.sourceforge.seqware.pipeline.runner.Runner
    443. 

  443.       --${metadata}
    444. 

  444.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    445. 

  445.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    446. 

  446.       --metadata-output-file-prefix ${output_prefix}
    447. 

  447.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    448. 

  448.       --module ${module}
    449. 

  449.       --
    450. 

  450.       --gcr-algorithm ${algo}
    451. 

  451.       --gcr-command ${java}
    452. 

  452.       -Xmx${picard_index_bam_mem}g
    453. 

  453.       -jar ${bin_dir}/${picardsort}
    454. 

  454.       INPUT=${data_dir}/gatk.realigned.${chr}.bam
    455. 

  455.       OUTPUT=${data_dir}/gatk.realigned.${chr}.queryname-sorted.bam
    456. 

  456.       SORT_ORDER=queryname
    457. 

  457.     </argument>
    458. 

  458. 

  459.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    460. 

  460.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    461. 

  461.     <profile namespace="globus" key="jobtype">condor</profile>
    462. 

  462.     <profile namespace="globus" key="count">${picard_slots}</profile>
    463. 

  463.     <profile namespace="globus" key="maxmemory">${picard_sort_mem + 4}000</profile>
    464. 

  464. 

  465.   </job>
    466. 

  466. 

  467.   <!-- Job: FixMates -->
    468. 

  468.   <#assign parentAlgo = "${algo}"/>
    469. 

  469.   <#assign algo = "FixMates"/>
    470. 

  470.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    471. 

  471.   <job id="ID40.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    472. 

  472.     <argument>
    473. 

  473.       -Xmx1000M
    474. 

  474.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    475. 

  475.       net.sourceforge.seqware.pipeline.runner.Runner
    476. 

  476.       --${metadata}
    477. 

  477.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    478. 

  478.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    479. 

  479.       --metadata-output-file-prefix ${output_prefix}
    480. 

  480.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    481. 

  481.       --module ${module}
    482. 

  482.       --
    483. 

  483.       --gcr-algorithm ${algo}
    484. 

  484.       --gcr-command ${java}
    485. 

  485.       -Xmx${picard_fixmate_mem}g
    486. 

  486.       -Djava.io.tmpdir=${tmp_dir}
    487. 

  487.       -jar ${bin_dir}/${picardfixmate} 
    488. 

  488.       INPUT=${data_dir}/gatk.realigned.${chr}.queryname-sorted.bam
    489. 

  489.       OUTPUT=${data_dir}/gatk.realigned.${chr}.fixmate.bam
    490. 

  490.       SO=coordinate
    491. 

  491.     </argument>
    492. 

  492. 

  493.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    494. 

  494.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    495. 

  495.     <profile namespace="globus" key="jobtype">condor</profile>
    496. 

  496.     <profile namespace="globus" key="count">${picard_slots}</profile>
    497. 

  497.     <profile namespace="globus" key="maxmemory">${picard_fixmate_mem + 4}000</profile>
    498. 

  498. 

  499.   </job>
    500. 

  500. 

  501.   <!-- Job: Index BAM: Can't we just have picard tools above do this? -->
    502. 

  502.   <#assign parentAlgo = "${algo}"/>
    503. 

  503.   <#assign algo = "IndexBam2"/>
    504. 

  504.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    505. 

  505.   <job id="ID50.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    506. 

  506.     <argument>
    507. 

  507.       -Xmx1000M
    508. 

  508.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    509. 

  509.       net.sourceforge.seqware.pipeline.runner.Runner
    510. 

  510.       --${metadata}
    511. 

  511.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    512. 

  512.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    513. 

  513.       --metadata-output-file-prefix ${output_prefix}
    514. 

  514.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    515. 

  515.       --module ${module}
    516. 

  516.       --
    517. 

  517.       --gcr-algorithm ${algo}
    518. 

  518.       --gcr-command ${java}
    519. 

  519.       -Xmx${picard_index_bam_mem}g
    520. 

  520.       -Djava.io.tmpdir=${tmp_dir}
    521. 

  521.       -jar ${bin_dir}/${picardindex}
    522. 

  522.       INPUT=${data_dir}/gatk.realigned.${chr}.fixmate.bam
    523. 

  523.     </argument>
    524. 

  524. 

  525.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    526. 

  526.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    527. 

  527.     <profile namespace="globus" key="jobtype">condor</profile>
    528. 

  528.     <profile namespace="globus" key="count">${picard_slots}</profile>
    529. 

  529.     <profile namespace="globus" key="maxmemory">${picard_index_bam_mem + 4}000</profile>
    530. 

  530. 

  531.   </job>
    532. 

  532. 

  533.   <!-- Job: MarkDuplicates -->
    534. 

  534.   <#assign parentAlgo = "${algo}"/>
    535. 

  535.   <#assign algo = "PicardMarkDuplicates"/>
    536. 

  536.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    537. 

  537.   <job id="ID55.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    538. 

  538.     <argument>
    539. 

  539.       -Xmx1000M
    540. 

  540.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    541. 

  541.       net.sourceforge.seqware.pipeline.runner.Runner
    542. 

  542.       --${metadata}
    543. 

  543.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    544. 

  544.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    545. 

  545.       --metadata-output-file-prefix ${output_prefix}
    546. 

  546.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    547. 

  547.       --module ${module}
    548. 

  548.       --
    549. 

  549.       --gcr-algorithm ${algo}
    550. 

  550.       --gcr-command ${java}
    551. 

  551.       -Xmx${picard_mark_dup_mem}g
    552. 

  552.       -jar ${bin_dir}/${picardmarkdups}
    553. 

  553.       INPUT=${data_dir}/gatk.realigned.${chr}.fixmate.bam
    554. 

  554.       OUTPUT=${data_dir}/gatk.realigned.${chr}.fixmate.markdups.bam
    555. 

  555.       CREATE_INDEX=true
    556. 

  556.       METRICS_FILE=${data_dir}/gatk.realigned.${chr}.fixmate.markdups.metrics
    557. 

  557.       VALIDATION_STRINGENCY=SILENT TMP_DIR=${tmp_dir}
    558. 

  558.     </argument>
    559. 

  559. 

  560.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    561. 

  561.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    562. 

  562.     <profile namespace="globus" key="jobtype">condor</profile>
    563. 

  563.     <profile namespace="globus" key="count">${picard_slots}</profile>
    564. 

  564.     <profile namespace="globus" key="maxmemory">${picard_mark_dup_mem + 4}000</profile>
    565. 

  565. 

  566.   </job>
    567. 

  567. 

  568. </#list>
    569. 

  569. <!-- END LOOP: by chromosome -->
    570. 

  570. 

  571. 

  572.   <!-- TODO: SO ROB POINTS OUT THAT COUNT COVARIANTS ACTUALLY ONLY WORKS ON A PER LANE BASIS SO WE COULD SPLIT BY THAT RG_ID (BY LANE) -->
    573. 

  573.   <!-- Job: Count Covariates -->
    574. 

  574.   <#assign parentAlgo = "PicardMarkDuplicates"/>
    575. 

  575.   <#assign algo = "CountCovariates"/>
    576. 

  576.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    577. 

  577.   <job id="ID60" namespace="seqware" name="runner" version="${seqware_version}">
    578. 

  578.     <argument>
    579. 

  579.       -Xmx1000M
    580. 

  580.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    581. 

  581.       net.sourceforge.seqware.pipeline.runner.Runner
    582. 

  582.       --${metadata}
    583. 

  583.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_accession
    584. 

  584.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    585. 

  585.       --metadata-output-file-prefix ${output_prefix}
    586. 

  586.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    587. 

  587.       --module ${module}
    588. 

  588.       --
    589. 

  589.       --gcr-algorithm ${algo}
    590. 

  590.       --gcr-command ${java}
    591. 

  591.       -Xmx${gatk_count_covariate_mem}g
    592. 

  592.       -Djava.io.tmpdir=${tmp_dir} 
    593. 

  593.       -jar ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    594. 

  594.       -l INFO
    595. 

  595.       -R ${ref_fasta}
    596. 

  596.       -knownSites ${gatk_dbsnp_vcf}
    597. 

  597. <#list chr_sizes?split(",") as chr_size>
    598. 

  598.   <#assign chrArr = chr_size?split(":")/>
    599. 

  599.   <#assign chr = chrArr[0]/>
    600. 

  600.   <#assign size = chrArr[1]?number/>
    601. 

  601.       -I ${data_dir}/gatk.realigned.${chr}.fixmate.markdups.bam
    602. 

  602. </#list>
    603. 

  603.       -T CountCovariates -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov DinucCovariate 
    604. 

  604.       -recalFile ${data_dir}/recal_data.csv -nt 8 -et NO_ET
    605. 

  605.     </argument>
    606. 

  606. 

  607. <!-- TODO: merge, do this on the combined bam files instead -->
    608. 

  608. 

  609.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    610. 

  610.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    611. 

  611.     <profile namespace="globus" key="jobtype">condor</profile>
    612. 

  612.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    613. 

  613.     <profile namespace="globus" key="maxmemory">${gatk_count_covariate_mem + 4}000</profile>
    614. 

  614. 

  615.   </job>
    616. 

  616. 

  617. 

  618. <!-- BEGIN LOOP: by chromosome -->
    619. 

  619. <#list chr_sizes?split(",") as chr_size>
    620. 

  620.   <#assign chrArr = chr_size?split(":")/>
    621. 

  621.   <#assign chr = chrArr[0]/>
    622. 

  622.   <#assign size = chrArr[1]?number/>
    623. 

  623. 

  624.   <!-- Job: Table Recal -->
    625. 

  625.   <#assign parentAlgo = "CountCovariates"/>
    626. 

  626.   <#assign algo = "TableRecalibration"/>
    627. 

  627.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    628. 

  628.   <job id="ID70.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    629. 

  629.     <argument>
    630. 

  630.       -Xmx1000M
    631. 

  631.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    632. 

  632.       net.sourceforge.seqware.pipeline.runner.Runner
    633. 

  633.       --${metadata}
    634. 

  634.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_accession
    635. 

  635.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    636. 

  636.       --metadata-output-file-prefix ${output_prefix}
    637. 

  637.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    638. 

  638.       --module ${module}
    639. 

  639.       --
    640. 

  640.       --gcr-algorithm ${algo}
    641. 

  641.       --gcr-command ${java}
    642. 

  642.       -Xmx${gatk_count_covariate_mem}g
    643. 

  643.       -Djava.io.tmpdir=${tmp_dir} 
    644. 

  644.       -jar ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    645. 

  645.       --preserve_qscores_less_than 2 -T TableRecalibration -l INFO -R ${ref_fasta}
    646. 

  646.       -I ${data_dir}/gatk.realigned.${chr}.fixmate.markdups.bam
    647. 

  647.       --out ${data_dir}/gatk.realigned.recal.${chr}.bam -recalFile ${data_dir}/recal_data.csv -L ${chr} -et NO_ET
    648. 

  648.     </argument>
    649. 

  649. 

  650.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    651. 

  651.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    652. 

  652.     <profile namespace="globus" key="jobtype">condor</profile>
    653. 

  653.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    654. 

  654.     <profile namespace="globus" key="maxmemory">${gatk_count_covariate_mem + 4}000</profile>
    655. 

  655. 

  656.   </job>
    657. 

  657. 

  658.   <!-- Job: Index BAM -->
    659. 

  659.   <#assign parentAlgo = "TableRecalibration"/>
    660. 

  660.   <#assign algo = "IndexBam3"/>
    661. 

  661.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    662. 

  662.   <job id="ID80.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    663. 

  663.     <argument>
    664. 

  664.       -Xmx1000M
    665. 

  665.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    666. 

  666.       net.sourceforge.seqware.pipeline.runner.Runner
    667. 

  667.       --${metadata}
    668. 

  668.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    669. 

  669.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    670. 

  670.       --metadata-output-file-prefix ${output_prefix}
    671. 

  671.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    672. 

  672.       --module ${module}
    673. 

  673.       --
    674. 

  674.       --gcr-algorithm ${algo}
    675. 

  675.       --gcr-command ${java}
    676. 

  676.       -Xmx${picard_index_bam_mem}g
    677. 

  677.       -Djava.io.tmpdir=${tmp_dir}
    678. 

  678.       -jar ${bin_dir}/${picardindex}
    679. 

  679.       INPUT=${data_dir}/gatk.realigned.recal.${chr}.bam
    680. 

  680.     </argument>
    681. 

  681. 

  682.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    683. 

  683.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    684. 

  684.     <profile namespace="globus" key="jobtype">condor</profile>
    685. 

  685.     <profile namespace="globus" key="count">${picard_slots}</profile>
    686. 

  686.     <profile namespace="globus" key="maxmemory">${picard_index_bam_mem + 4}000</profile>
    687. 

  687. 

  688.   </job>
    689. 

  689. 

  690.   <!-- Job: Unified Genotyper SNP caller -->
    691. 

  691.   <!-- FIXME: it seems like I can only use -nt 1 according to http://getsatisfaction.com/gsa/topics/genotyper_error_unable_to_create_basicfeaturereader_using_feature_file -->
    692. 

  692.   <#assign parentAlgo = "IndexBam3"/>
    693. 

  693.   <#assign algo = "GATKUnifiedGenotyperSNV"/>
    694. 

  694.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    695. 

  695.   <job id="ID90.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    696. 

  696.     <argument>
    697. 

  697.       -Xmx1000M
    698. 

  698.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    699. 

  699.       net.sourceforge.seqware.pipeline.runner.Runner
    700. 

  700.       --${metadata}
    701. 

  701.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    702. 

  702.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    703. 

  703.       --metadata-output-file-prefix ${output_prefix}
    704. 

  704.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    705. 

  705.       --module ${module}
    706. 

  706.       --
    707. 

  707.       --gcr-algorithm ${algo}
    708. 

  708.       --gcr-command ${java}
    709. 

  709.       -Xmx${gatk_unified_genotyper_mem}g
    710. 

  710.       -Djava.io.tmpdir=${tmp_dir}
    711. 

  711.       -jar ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    712. 

  712.       -R ${ref_fasta}
    713. 

  713.       -T UnifiedGenotyper
    714. 

  714.       -I ${data_dir}/gatk.realigned.recal.${chr}.bam
    715. 

  715.       -D ${gatk_dbsnp_vcf}
    716. 

  716.       -o ${data_dir}/gatk.realigned.recal.bam.snps.raw.${chr}.vcf
    717. 

  717.       -stand_call_conf 30 -stand_emit_conf 1.0 -metrics ${data_dir}/gatk.realigned.recal.bam.snps.raw.${chr}.metrics
    718. 

  718.       -nt 1 -L ${chr} -et NO_ET
    719. 

  719.     </argument>
    720. 

  720. 

  721.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    722. 

  722.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    723. 

  723.     <profile namespace="globus" key="jobtype">condor</profile>
    724. 

  724.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    725. 

  725.     <profile namespace="globus" key="maxmemory">${gatk_unified_genotyper_mem + 4}000</profile>
    726. 

  726. 

  727.   </job>
    728. 

  728. 

  729.  <!-- TODO: move this to the SomaticIndelDetector and use "unpaired" to paramaterize, "minFraction .3", "minCoverage 4" -->
    730. 

  730.  <!-- see http://www.broadinstitute.org/gsa/wiki/index.php/Somatic_Indel_Detector -->
    731. 

  731.  
    732. 

  732. 

  733.   <!-- Job: Indel caller -->
    734. 

  734.   <#assign parentAlgo = "IndexBam3"/>
    735. 

  735.   <#assign algo = "GATKUnifiedGenotyperIndel"/>
    736. 

  736.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    737. 

  737.   <job id="ID100.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    738. 

  738.     <argument>
    739. 

  739.       -Xmx1000M
    740. 

  740.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    741. 

  741.       net.sourceforge.seqware.pipeline.runner.Runner
    742. 

  742.       --${metadata}
    743. 

  743.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    744. 

  744.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    745. 

  745.       --metadata-output-file-prefix ${output_prefix}
    746. 

  746.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    747. 

  747.       --module ${module}
    748. 

  748.       --
    749. 

  749.       --gcr-algorithm ${algo}
    750. 

  750.       --gcr-command ${java}
    751. 

  751.       -Xmx${gatk_indel_genotyper_mem}g
    752. 

  752.       -Djava.io.tmpdir=${tmp_dir}
    753. 

  753.       -jar ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    754. 

  754.       -T UnifiedGenotyper
    755. 

  755.       -l INFO
    756. 

  756.       -R ${ref_fasta}
    757. 

  757.       -I ${data_dir}/gatk.realigned.recal.${chr}.bam
    758. 

  758.       -o ${data_dir}/gatk.realigned.recal.bam.indels.raw.${chr}.vcf
    759. 

  759.       -glm INDEL -G Standard -stand_emit_conf 10 -stand_call_conf 50 -dcov 1000 
    760. 

  760.       -metrics ${data_dir}/gatk.realigned.recal.bam.indels.raw.${chr}.metrics
    761. 

  761.       -D ${gatk_dbsnp_vcf}
    762. 

  762.       -L ${chr} -et NO_ET
    763. 

  763.     </argument>
    764. 

  764. 

  765.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    766. 

  766.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    767. 

  767.     <profile namespace="globus" key="jobtype">condor</profile>
    768. 

  768.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    769. 

  769.     <profile namespace="globus" key="maxmemory">${gatk_indel_genotyper_mem + 4}000</profile>
    770. 

  770. 

  771.   </job>
    772. 

  772. 

  773.   <!-- Job: Indel Filter -->
    774. 

  774.   <#assign parentAlgo = "GATKUnifiedGenotyperIndel"/>
    775. 

  775.   <#assign algo = "GATKUnifiedGenotyperIndelFilter"/>
    776. 

  776.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    777. 

  777.   <job id="ID110.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    778. 

  778.     <argument>
    779. 

  779.       -Xmx1000M
    780. 

  780.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    781. 

  781.       net.sourceforge.seqware.pipeline.runner.Runner
    782. 

  782.       --${metadata}
    783. 

  783.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    784. 

  784.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    785. 

  785.       --metadata-output-file-prefix ${output_prefix}
    786. 

  786.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    787. 

  787.       --module ${module}
    788. 

  788.       --
    789. 

  789.       --gcr-algorithm ${algo}
    790. 

  790.       --gcr-command bash 
    791. 

  791.       ${workflow_bundle_dir}/${workflow_name}/bin/sw_module_gatk_indel_filter.sh
    792. 

  792.       ${java}
    793. 

  793.       ${gatk_variant_filter_mem} 
    794. 

  794.       ${tmp_dir}
    795. 

  795.       ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    796. 

  796.       ${ref_fasta}
    797. 

  797.       ${data_dir}/gatk.realigned.recal.bam.indels.raw.${chr}.vcf 
    798. 

  798.       ${data_dir}/gatk.realigned.recal.bam.indels.filtered.${chr}.vcf
    799. 

  799.       ${chr}
    800. 

  800.     </argument>
    801. 

  801. 

  802.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    803. 

  803.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    804. 

  804.     <profile namespace="globus" key="jobtype">condor</profile>
    805. 

  805.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    806. 

  806.     <profile namespace="globus" key="maxmemory">${gatk_variant_filter_mem + 4}000</profile>
    807. 

  807. 

  808.   </job>
    809. 

  809. 

  810.   <!-- Job: SNV filter -->
    811. 

  811.   <!-- FIXME: will need a WGS version -->
    812. 

  812.   <#assign parentAlgo = "GATKUnifiedGenotyperSNV"/>
    813. 

  813.   <#assign algo = "GATKUnifiedGenotyperSNVFilter"/>
    814. 

  814.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    815. 

  815.   <job id="ID120.${chr_size_index}" namespace="seqware" name="runner" version="${seqware_version}">
    816. 

  816.     <argument>
    817. 

  817.       -Xmx1000M
    818. 

  818.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    819. 

  819.       net.sourceforge.seqware.pipeline.runner.Runner
    820. 

  820.       --${metadata}
    821. 

  821.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    822. 

  822.       --metadata-processing-accession-file ${accession_dir}/${algo}_${chr}_accession
    823. 

  823.       --metadata-output-file-prefix ${output_prefix}
    824. 

  824.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    825. 

  825.       --module ${module}
    826. 

  826.       --
    827. 

  827.       --gcr-algorithm ${algo}
    828. 

  828.       --gcr-command bash
    829. 

  829.       ${workflow_bundle_dir}/${workflow_name}/bin/sw_module_gatk_snv_filter.sh
    830. 

  830.       ${java}
    831. 

  831.       ${gatk_variant_filter_mem}
    832. 

  832.       ${tmp_dir}
    833. 

  833.       ${bin_dir}/GenomeAnalysisTK-1.3-16-g6a5d5e7/GenomeAnalysisTK.jar
    834. 

  834.       ${ref_fasta}
    835. 

  835.       ${data_dir}/gatk.realigned.recal.bam.snps.raw.${chr}.vcf
    836. 

  836.       ${data_dir}/gatk.realigned.recal.bam.snps.filtered.${chr}.vcf
    837. 

  837.       ${chr}
    838. 

  838.       ${data_dir}/gatk.realigned.recal.bam.indels.raw.${chr}.vcf 
    839. 

  839.     </argument>
    840. 

  840. 

  841.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    842. 

  842.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    843. 

  843.     <profile namespace="globus" key="jobtype">condor</profile>
    844. 

  844.     <profile namespace="globus" key="count">${gatk_slots}</profile>
    845. 

  845.     <profile namespace="globus" key="maxmemory">${gatk_variant_filter_mem + 4}000</profile>
    846. 

  846. 

  847.   </job>
    848. 

  848. 

  849. </#list>
    850. 

  850. <!-- END LOOP: by chromosome -->
    851. 

  851. 

  852.   <!-- Job: merge SNV -->
    853. 

  853.   <#assign parentAlgo = "GATKUnifiedGenotyperSNV"/>
    854. 

  854.   <#assign algo = "MergeRawSNV"/>
    855. 

  855.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    856. 

  856.   <job id="ID130" namespace="seqware" name="runner" version="${seqware_version}">
    857. 

  857.     <argument>
    858. 

  858.       -Xmx1000M
    859. 

  859.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    860. 

  860.       net.sourceforge.seqware.pipeline.runner.Runner
    861. 

  861.       --${metadata}
    862. 

  862. <#list chr_sizes?split(",") as chr_size>
    863. 

  863.   <#assign chrArr = chr_size?split(":")/>
    864. 

  864.   <#assign chr = chrArr[0]/>
    865. 

  865.   <#assign size = chrArr[1]?number/>
    866. 

  866.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    867. 

  867. </#list>
    868. 

  868.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    869. 

  869.       --metadata-output-file-prefix ${output_prefix}
    870. 

  870.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    871. 

  871.       --module ${module}
    872. 

  872.       --
    873. 

  873.       --gcr-algorithm ${algo}
    874. 

  874.       --gcr-command ${perl}
    875. 

  875.       ${workflow_bundle_dir}/${workflow_name}/bin/sw_module_merge_GATK_VCF.pl
    876. 

  876. <#list chr_sizes?split(",") as chr_size>
    877. 

  877.   <#assign chrArr = chr_size?split(":")/>
    878. 

  878.   <#assign chr = chrArr[0]/>
    879. 

  879.   <#assign size = chrArr[1]?number/>
    880. 

  880.       --vcf-input-file ${data_dir}/gatk.realigned.recal.bam.snps.raw.${chr}.vcf
    881. 

  881. </#list>
    882. 

  882.       --vcf-output-file ${data_dir}/gatk.realigned.recal.bam.snps.raw.merged.vcf
    883. 

  883.     </argument>
    884. 

  884. 

  885.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    886. 

  886.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    887. 

  887.     <profile namespace="globus" key="jobtype">condor</profile>
    888. 

  888.     <profile namespace="globus" key="count">1</profile>
    889. 

  889.     <profile namespace="globus" key="maxmemory">2000</profile>
    890. 

  890. 

  891.   </job>
    892. 

  892. 

  893. <!-- TODO: add a annotation step  for things like overlaps with indel --> 
    894. 

  894. 

  895.   <!-- Job: merge filtered SNV -->
    896. 

  896.   <#assign parentAlgo = "GATKUnifiedGenotyperSNVFilter"/>
    897. 

  897.   <#assign algo = "MergeFilteredSNV"/>
    898. 

  898.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    899. 

  899.   <job id="ID140" namespace="seqware" name="runner" version="${seqware_version}">
    900. 

  900.     <argument>
    901. 

  901.       -Xmx1000M
    902. 

  902.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    903. 

  903.       net.sourceforge.seqware.pipeline.runner.Runner
    904. 

  904.       --${metadata}
    905. 

  905. <#list chr_sizes?split(",") as chr_size>
    906. 

  906.   <#assign chrArr = chr_size?split(":")/>
    907. 

  907.   <#assign chr = chrArr[0]/>
    908. 

  908.   <#assign size = chrArr[1]?number/>
    909. 

  909.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    910. 

  910. </#list>
    911. 

  911.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    912. 

  912.       --metadata-output-file-prefix ${output_prefix}
    913. 

  913.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    914. 

  914.       --module ${module}
    915. 

  915.       --
    916. 

  916.       --gcr-algorithm ${algo}
    917. 

  917.       --gcr-command ${perl}
    918. 

  918.       ${workflow_bundle_dir}/${workflow_name}/bin/sw_module_merge_GATK_VCF.pl
    919. 

  919. <#list chr_sizes?split(",") as chr_size>
    920. 

  920.   <#assign chrArr = chr_size?split(":")/>
    921. 

  921.   <#assign chr = chrArr[0]/>
    922. 

  922.   <#assign size = chrArr[1]?number/>
    923. 

  923.       --vcf-input-file ${data_dir}/gatk.realigned.recal.bam.snps.filtered.${chr}.vcf
    924. 

  924. </#list>
    925. 

  925.       --vcf-output-file ${data_dir}/gatk.realigned.recal.bam.snps.filtered.merged.vcf
    926. 

  926.     </argument>
    927. 

  927. 

  928.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    929. 

  929.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    930. 

  930.     <profile namespace="globus" key="jobtype">condor</profile>
    931. 

  931.     <profile namespace="globus" key="count">1</profile>
    932. 

  932.     <profile namespace="globus" key="maxmemory">2000</profile>
    933. 

  933. 

  934.   </job>
    935. 

  935. 

  936. 

  937.   <!-- Job: merge indels -->
    938. 

  938.   <#assign parentAlgo = "GATKUnifiedGenotyperIndel"/>
    939. 

  939.   <#assign algo = "MergeRawIndel"/>
    940. 

  940.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    941. 

  941.   <job id="ID150" namespace="seqware" name="runner" version="${seqware_version}">
    942. 

  942.     <argument>
    943. 

  943.       -Xmx1000M
    944. 

  944.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    945. 

  945.       net.sourceforge.seqware.pipeline.runner.Runner
    946. 

  946.       --${metadata}
    947. 

  947. <#list chr_sizes?split(",") as chr_size>
    948. 

  948.   <#assign chrArr = chr_size?split(":")/>
    949. 

  949.   <#assign chr = chrArr[0]/>
    950. 

  950.   <#assign size = chrArr[1]?number/>
    951. 

  951.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    952. 

  952. </#list>
    953. 

  953.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    954. 

  954.       --metadata-output-file-prefix ${output_prefix}
    955. 

  955.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    956. 

  956.       --module ${module}
    957. 

  957.       --
    958. 

  958.       --gcr-algorithm ${algo}
    959. 

  959.       --gcr-command ${perl}
    960. 

  960.       ${workflow_bundle_dir}/${workflow_name}/bin/sw_module_merge_GATK_VCF.pl
    961. 

  961. <#list chr_sizes?split(",") as chr_size>
    962. 

  962.   <#assign chrArr = chr_size?split(":")/>
    963. 

  963.   <#assign chr = chrArr[0]/>
    964. 

  964.   <#assign size = chrArr[1]?number/>
    965. 

  965.       --vcf-input-file ${data_dir}/gatk.realigned.recal.bam.indels.raw.${chr}.vcf
    966. 

  966. </#list>
    967. 

  967.       --vcf-output-file ${data_dir}/gatk.realigned.recal.bam.indels.raw.merged.vcf
    968. 

  968.     </argument>
    969. 

  969. 

  970.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    971. 

  971.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    972. 

  972.     <profile namespace="globus" key="jobtype">condor</profile>
    973. 

  973.     <profile namespace="globus" key="count">1</profile>
    974. 

  974.     <profile namespace="globus" key="maxmemory">2000</profile>
    975. 

  975. 

  976.   </job>
    977. 

  977. 

  978. 

  979.   <!-- Job: merge filtered Indel -->
    980. 

  980.   <#assign parentAlgo = "GATKUnifiedGenotyperIndelFilter"/>
    981. 

  981.   <#assign algo = "MergeFilteredIndel"/>
    982. 

  982.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    983. 

  983.   <job id="ID160" namespace="seqware" name="runner" version="${seqware_version}">
    984. 

  984.     <argument>
    985. 

  985.       -Xmx1000M
    986. 

  986.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    987. 

  987.       net.sourceforge.seqware.pipeline.runner.Runner
    988. 

  988.       --${metadata}
    989. 

  989. <#list chr_sizes?split(",") as chr_size>
    990. 

  990.   <#assign chrArr = chr_size?split(":")/>
    991. 

  991.   <#assign chr = chrArr[0]/>
    992. 

  992.   <#assign size = chrArr[1]?number/>
    993. 

  993.       --metadata-parent-accession-file ${accession_dir}/${parentAlgo}_${chr}_accession
    994. 

  994. </#list>
    995. 

  995.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    996. 

  996.       --metadata-output-file-prefix ${output_prefix}
    997. 

  997.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    998. 

  998.       --module ${module}
    999. 

  999.       --
    1000. 

  1000.       --gcr-algorithm ${algo}
    1001. 

  1001.       --gcr-command ${perl}
    1002. 

  1002.       ${workflow_bundle_dir}/${workflow_name}/bin/sw_module_merge_GATK_VCF.pl
    1003. 

  1003. <#list chr_sizes?split(",") as chr_size>
    1004. 

  1004.   <#assign chrArr = chr_size?split(":")/>
    1005. 

  1005.   <#assign chr = chrArr[0]/>
    1006. 

  1006.   <#assign size = chrArr[1]?number/>
    1007. 

  1007.       --vcf-input-file ${data_dir}/gatk.realigned.recal.bam.indels.filtered.${chr}.vcf
    1008. 

  1008. </#list>
    1009. 

  1009.       --vcf-output-file ${data_dir}/gatk.realigned.recal.bam.indels.filtered.merged.vcf
    1010. 

  1010.     </argument>
    1011. 

  1011. 

  1012.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    1013. 

  1013.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    1014. 

  1014.     <profile namespace="globus" key="jobtype">condor</profile>
    1015. 

  1015.     <profile namespace="globus" key="count">1</profile>
    1016. 

  1016.     <profile namespace="globus" key="maxmemory">2000</profile>
    1017. 

  1017. 

  1018.   </job>
    1019. 

  1019. 

  1020. 

  1021.   <!-- TODO: need to add an annotation step that works off of the filtered SNV VCF file and the filtered Indel VCF file as inputs that does a filter to annotate these files where indels and snvs overlap -->
    1022. 

  1022. 

  1023.   <!-- Job: merge raw variants ID150 130-->
    1024. 

  1024.   <#assign algo = "MergeRawVariants"/>
    1025. 

  1025.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    1026. 

  1026.   <job id="ID170" namespace="seqware" name="runner" version="${seqware_version}">
    1027. 

  1027.     <argument>
    1028. 

  1028.       -Xmx1000M
    1029. 

  1029.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/seqware-pipeline-${seqware_version}.jar
    1030. 

  1030.       net.sourceforge.seqware.pipeline.runner.Runner
    1031. 

  1031.       --${metadata}
    1032. 

  1032.       --metadata-parent-accession-file ${accession_dir}/MergeRawIndel_accession
    1033. 

  1033.       --metadata-parent-accession-file ${accession_dir}/MergeRawSNV_accession
    1034. 

  1034.       --metadata-processing-accession-file ${accession_dir}/${algo}_accession
    1035. 

  1035.       --metadata-output-file-prefix ${output_prefix}
    1036. 

  1036.       --metadata-workflow-run-ancestor-accession ${workflow_run_accession}
    1037. 

  1037.       --module ${module}
    1038. 

  1038.       --
    1039. 

  1039.       --gcr-algorithm ${algo}
    1040. 

  1040.       --gcr-output-file ${algo}:text/vcf-4:${output_dir}/seqware-${seqware_version}_GATKREcalibrationAndVariantCalling-${workflow_version}/${random}/${identifier}.gatk.realigned.recal.bam.variants.raw.merged.vcf
    1041. 

  1041.       --gcr-command ${perl}
    1042. 

  1042.       ${workflow_bundle_dir}/${workflow_name}/bin/sw_module_merge_GATK_VCF.pl
    1043. 

  1043.       --vcf-input-file ${data_dir}/gatk.realigned.recal.bam.snps.raw.merged.vcf
    1044. 

  1044.       --vcf-input-file ${data_dir}/gatk.realigned.recal.bam.indels.raw.merged.vcf
    1045. 

  1045.       --vcf-output-file ${output_dir}/seqware-${seqware_version}_GATKREcalibrationAndVariantCalling-${workflow_version}/${random}/${identifier}.gatk.realigned.recal.bam.variants.raw.merged.vcf
    1046. 

  1046.     </argument>
    1047. 

  1047. 

  1048.     <!-- See http://www.globus.org/api/c-globus-4.0.3/globus_gram_job_manager/html/globus_job_manager_rsl.html -->
    1049. 

  1049.     <!-- See http://pegasus.isi.edu/wms/docs/3.0/advanced_concepts_profiles.php#id2738647 -->
    1050. 

  1050.     <profile namespace="globus" key="jobtype">condor</profile>
    1051. 

  1051.     <profile namespace="globus" key="count">1</profile>
    1052. 

  1052.     <profile namespace="globus" key="maxmemory">2000</profile>
    1053. 

  1053. 

  1054.     <@requires_dir "${output_dir}/seqware-${seqware_version}_GATKREcalibrationAndVariantCalling-${workflow_version}/${random}"/>
    1055. 

  1055. 

  1056.   </job>
    1057. 

  1057. 

  1058. 

  1059.   <!-- Job: merge filtered variants 140 160-->
    1060. 

  1060.   <#assign algo = "MergeFilteredVariants"/>
    1061. 

  1061.   <#assign module = "net.sourceforge.seqware.pipeline.modules.GenericCommandRunner"/>
    1062. 

  1062.   <job id="ID180" namespace="seqware" name="runner" version="${seqware_version}">
    1063. 

  1063.     <argument>
    1064. 

  1064.       -Xmx1000M
    1065. 

  1065.       -classpath ${workflow_bundle_dir}/${workflow_name}/classes:${workflow_bundle_dir}/${workflow_name}/lib/…
    1066.

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