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import "./tasks/processSomatic.wdl" as processSomatic |
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import "./tasks/processSomatic.wdl" as processSomatic |
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import "./tasks/somaticFilter.wdl" as somaticFilter |
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import "./tasks/somaticFilter.wdl" as somaticFilter |
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import "./tasks/replaceRG.wdl" as replaceRG |
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import "./tasks/replaceRG.wdl" as replaceRG |
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import "./tasks/pindel.wdl" as pindel |
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import "./tasks/Pindel.wdl" as Pindel |
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import "./tasks/ANNOVAR.wdl" as ANNOVAR |
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import "./tasks/ANNOVAR.wdl" as ANNOVAR |
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import "./tasks/VEP.wdl" as VEP |
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import "./tasks/VEP.wdl" as VEP |
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} |
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} |
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if (pindel) { |
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if (pindel) { |
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call pindel.pindel as pindel { |
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call Pindel.Pindel as Pindel { |
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input: |
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input: |
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sample_id=sample_id + '.N', |
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sample_id=sample_id + '.N', |
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bam=normal_BQSR.recaled_bam, |
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bam=normal_BQSR.recaled_bam, |
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} |
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} |
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if (pindel) { |
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if (pindel) { |
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call pindel.pindel as pindel_fb { |
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call Pindel.Pindel as Pindel_fb { |
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input: |
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input: |
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sample_id=sample_id + '.N', |
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sample_id=sample_id + '.N', |
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bam=normal_BQSR_fb.recaled_bam, |
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bam=normal_BQSR_fb.recaled_bam, |