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release_and_pulldown.wdl
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workflow release_and_pulldown{
File adna_jar
File picard_jar
File python_release_libraries
File python_pulldown
File python_read_groups_from_bam
File report
File nuclear_bamlist
File mt_bamlist
String release_parent_directory
String label
call build_release_libraries as build_mt{input:
bamlist = mt_bamlist,
adna_jar = adna_jar,
picard_jar = picard_jar,
python_release_libraries = python_release_libraries,
python_read_groups_from_bam = python_read_groups_from_bam,
release_parent_directory = release_parent_directory,
minutes = 80
}
call build_release_libraries as build_nuclear{input:
bamlist = nuclear_bamlist,
adna_jar = adna_jar,
picard_jar = picard_jar,
python_release_libraries = python_release_libraries,
python_read_groups_from_bam = python_read_groups_from_bam,
release_parent_directory= release_parent_directory
}
call pulldown{ input:
bamlist = nuclear_bamlist,
report = report,
python_pulldown = python_pulldown,
python_release_libraries = python_release_libraries,
python_read_groups_from_bam = python_read_groups_from_bam,
release_parent_directory = release_parent_directory,
label = label,
unused = build_nuclear.unused
}
}
task build_release_libraries{
File bamlist
File adna_jar
File picard_jar
File python_release_libraries
File python_read_groups_from_bam
String release_parent_directory
Int processes = 8
Int minutes = 720
command{
python3 ${python_release_libraries} --num_threads ${processes} --release_directory ${release_parent_directory} ${bamlist} ${adna_jar} ${picard_jar} > out
}
output{
File unused = "out"
}
runtime{
cpus: processes
runtime_minutes: minutes
requested_memory_mb_per_core: 6000
}
}
task pulldown{
File bamlist
File report
File pulldown_executable
File python_pulldown
File python_release_libraries
File python_read_groups_from_bam
File python_merge_pulldown
String release_parent_directory
String label
String? snp_set
File unused
command{
python3 ${python_pulldown} --pulldown_executable ${pulldown_executable} --pulldown_label ${label} --release_directory ${release_parent_directory} ${"--snp_set " + snp_set} ${bamlist} ${report}
}
output{
File pulldown_ind = "${label}.combined.ind"
File pulldown_snp = "${label}.combined.snp"
File pulldown_geno = "${label}.combined.geno"
File dblist = "${label}.dblist"
}
runtime{
cpus: 2
requested_memory_mb_per_core: 8000
}
}