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tasks/Manta.wdl
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| MANTA_ANALYSIS_PATH="/cromwell_root/tmp" | MANTA_ANALYSIS_PATH="/cromwell_root/tmp" | ||||
| mkdir -p $MANTA_ANALYSIS_PATH | mkdir -p $MANTA_ANALYSIS_PATH | ||||
| cp ${regions} my_baits.bed | |||||
| # Double check: sort the bed file | |||||
| sort -k1,1V -k2,2n -k3,3n ${regions} > my_baits.bed | |||||
| bgzip -c my_baits.bed > my_baits.bed.gz | bgzip -c my_baits.bed > my_baits.bed.gz | ||||
| tabix -p bed my_baits.bed.gz | tabix -p bed my_baits.bed.gz | ||||
| # input files | # input files |
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