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Merge pull request #41 from dozy/fixmate_markdups_calibration
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Fixmate, streaming markdups, seq error reports, template library
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@dkj
dkj committed Oct 14, 2014
2 parents a721771 + 7f57714 commit bdf9711
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Showing 8 changed files with 206 additions and 1,202 deletions.
180 changes: 90 additions & 90 deletions data/bwamem_wtsi_stage2_template.vtf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,46 +2,18 @@
"description":"Process DNA seq data in BAM files within NPG Pipeline producing WTSI DNAP Sequencing Informatics BAM output: full PG history, complete SQ lines, adapter marking, recoding indexing sequence etc",
"nodes":[
{
"id":"bmd_phix_tee0",
"id":"bmd_phix_multiway",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":"teepot -w 300 __OUT1__ __OUT2__"
"cmd":"teepot -w 300 __SCRAMBLE_OUT__ __BAMCHECK_OUT__ __FLAGSTAT_OUT__ __CALIBRATION_PU_OUT__ __BAM_OUT__"
},
{
"id":"bmd_tee1",
"id":"bmd_target_multiway",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":"teepot -w 300 __OUT1__ __OUT2__"
},
{
"id":"bmd_tee2",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":"teepot -w 300 __OUT1__ __OUT2__"
},
{
"id":"bmd_tee3",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":"teepot -w 300 __OUT1__ __OUT2__"
},
{
"id":"bmd_phix_tee1",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":"teepot -w 300 __OUT1__ __OUT2__"
},
{
"id":"bmd_phix_tee2",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":"teepot -w 300 __OUT1__ __OUT2__"
"cmd":"teepot -w 300 __SCRAMBLE_OUT__ __BAMCHECK_OUT__ __FLAGSTAT_OUT__ __CALIBRATION_PU_OUT__ __BAM_OUT__"
},
{
"id":"scramble",
Expand Down Expand Up @@ -79,6 +51,66 @@
"use_STDOUT": true,
"cmd":"scramble -I bam -O cram -r __REFERENCE_GENOME__"
},
{
"id":"calibration_pu_target",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":{"subst_param_name":"calibration_pu_target_cmd",
"required":"yes",
"subst_constructor":{
"vals":[
{"subst_param_name":"calibration_pu_executable","required":"no","default":"calibration_pu"},
"-p",
{"subst_param_name":"calibration_pu_target_prefix",
"required":"yes",
"subst_constructor":{
"vals":[
{"subst_param_name":"outdatadir","required":"no","default":"."},
"/",
{"subst_param_name":"rpt","required":"yes"},
{"subst_param_name":"bam_ext","required":"no","default":".bam"}
],
"postproc":{"op":"concat", "pad":""}
}
},
"-filter-bad-tiles",{"subst_param_name":"calibration_pu_bad_tiles_count","required":"no","default":"2"},
"-"
],
"postproc":{"op":"pack","pad":" "}
}
}
},
{
"id":"calibration_pu_phix",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": false,
"cmd":{"subst_param_name":"calibration_pu_phix_cmd",
"required":"yes",
"subst_constructor":{
"vals":[
{"subst_param_name":"calibration_pu_executable","required":"no","default":"calibration_pu"},
"-p",
{"subst_param_name":"calibration_pu_phix_prefix",
"required":"yes",
"subst_constructor":{
"vals":[
{"subst_param_name":"outdatadir","required":"no","default":"."},
"/",
{"subst_param_name":"rpt","required":"yes"},
{"subst_param_name":"phix_bam_ext","required":"no","default":"_phix.bam"}
],
"postproc":{"op":"concat", "pad":""}
}
},
"-filter-bad-tiles",{"subst_param_name":"calibration_pu_bad_tiles_count","required":"no","default":"2"},
"-"
],
"postproc":{"op":"pack","pad":" "}
}
}
},
{
"id":"bamcheck_phix",
"type":"EXEC",
Expand Down Expand Up @@ -453,9 +485,6 @@
"use_STDOUT": true,
"cmd":"bam12auxmerge level=0 rankstrip=1 ranksplit=0 zztoname=0 clipreinsert=1 __PREALN_BAM__"
},
#####################################
# alignment filter and metrics output
#####################################
{
"id":"alignment_filter",
"type":"EXEC",
Expand Down Expand Up @@ -511,15 +540,12 @@
}
}
},
#######################
# phiX final processing
#######################
{
"id":"bamsort_coord_phix",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"bamsort SO=coordinate level=0"
"cmd":"bamsort level=0 verbose=0 SO=coordinate fixmates=1 adddupmarksupport=1"
},
{
"id":"bammarkduplicates_phix",
Expand All @@ -530,8 +556,9 @@
"required":"yes",
"subst_constructor":{
"vals":[
"bammarkduplicates ",
"bamstreamingmarkduplicates ",
"level=0 ",
"verbose=0 ",
"M=",
{"subst_param_name":"outdatadir","required":"no","default":"."},
"/",
Expand Down Expand Up @@ -584,15 +611,12 @@
}
}
},
#############################
# target BAM final processing
#############################
{
"id":"bamsort_coord_target",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"bamsort SO=coordinate level=0"
"cmd":"bamsort level=0 verbose=0 SO=coordinate fixmates=1 adddupmarksupport=1"
},
{
"id":"bammarkduplicates_target",
Expand All @@ -603,8 +627,9 @@
"required":"yes",
"subst_constructor":{
"vals":[
"bammarkduplicates ",
"bamstreamingmarkduplicates ",
"level=0 ",
"verbose=0 ",
"M=",
{"subst_param_name":"outdatadir","required":"no","default":"."},
"/",
Expand Down Expand Up @@ -656,9 +681,6 @@
}
}
},
##################################################
# check input primary/sequence data matches output
##################################################
{
"id":"bamcat_output",
"type":"EXEC",
Expand Down Expand Up @@ -703,68 +725,58 @@
{
"id":"bammarkduplicates_phix_to_tee",
"from":"bammarkduplicates_phix",
"to":"bmd_phix_tee0"
},
{
"id":"bmd_phix_tee0_to_bmd_phix_tee0",
"from":"bmd_phix_tee0:__OUT2__",
"to":"bmd_phix_tee1"
"to":"bmd_phix_multiway"
},
{
"id":"bammarkduplicates_to_tee",
"from":"bammarkduplicates_target",
"to":"bmd_tee1"
"to":"bmd_target_multiway"
},
{
"id":"tee_to_scramble_phix",
"from":"bmd_phix_tee1:__OUT2__",
"from":"bmd_phix_multiway:__SCRAMBLE_OUT__",
"to":"scramble_phix"
},
{
"id":"tee_to_scramble",
"from":"bmd_tee1:__OUT2__",
"from":"bmd_target_multiway:__SCRAMBLE_OUT__",
"to":"scramble"
},
{
"id":"bmd_phix_tee1_to_bmd_phix_tee2",
"from":"bmd_phix_tee1:__OUT1__",
"to":"bmd_phix_tee2"
},
{
"id":"bmd_tee1_to_bmd_tee2",
"from":"bmd_tee1:__OUT1__",
"to":"bmd_tee2"
},
{
"id":"tee_phix_to_bamcheck_phix",
"from":"bmd_phix_tee2:__OUT1__",
"from":"bmd_phix_multiway:__BAMCHECK_OUT__",
"to":"bamcheck_phix"
},
{
"id":"tee_to_bamcheck",
"from":"bmd_tee2:__OUT2__",
"from":"bmd_target_multiway:__BAMCHECK_OUT__",
"to":"bamcheck"
},
{
"id":"bmd_tee2_to_bmd_tee3",
"from":"bmd_tee2:__OUT1__",
"to":"bmd_tee3"
},
{
"id":"bmd_tee2_phix_to_flagstat",
"from":"bmd_phix_tee2:__OUT2__",
"from":"bmd_phix_multiway:__FLAGSTAT_OUT__",
"to":"flagstat_phix"
},
{
"id":"bmd_tee3_to_flagstat_filter",
"from":"bmd_tee3:__OUT2__",
"from":"bmd_target_multiway:__FLAGSTAT_OUT__",
"to":"flagstat_filter"
},
{
"id":"flagstat_filter_to_flagstat",
"from":"flagstat_filter",
"to":"flagstat"
},
{
"id":"bmd_mw_phix_to_calibration_pu",
"from":"bmd_phix_multiway:__CALIBRATION_PU_OUT__",
"to":"calibration_pu_phix"
},
{
"id":"bmd_mw_to_calibration_pu",
"from":"bmd_target_multiway:__CALIBRATION_PU_OUT__",
"to":"calibration_pu_target"
},
{
"id":"scramble_to_phix_cram",
"from":"scramble_phix",
Expand Down Expand Up @@ -918,9 +930,6 @@
{
"id":"bam12auxmerge_to_alignment_filter",
"from":"bam12auxmerge",
#################
# AlignmentFilter
#################
"to":"alignment_filter:__TARGET_INBAM__"
},
{
Expand All @@ -933,9 +942,6 @@
"from":"alignment_filter:__AF_METRICS__",
"to":"af_metrics"
},
#####################
# phiX BAM production
#####################
{
"id":"alignmentfilter_to_bamsort_coord_phix",
"from":"alignment_filter:__PHIX_OUTBAM__",
Expand All @@ -948,17 +954,14 @@
},
{
"id":"bmd_phix_tee0_to_bamrecompress_phix",
"from":"bmd_phix_tee0:__OUT1__",
"from":"bmd_phix_multiway:__BAM_OUT__",
"to":"bamrecompress_phix"
},
{
"id":"bamrecompress_to_pb",
"from":"bamrecompress_phix",
"to":"phix_bam"
},
#######################
# Target BAM production
#######################
{
"id":"alignmentfilter_to_bamsort_coord_target",
"from":"alignment_filter",
Expand All @@ -971,17 +974,14 @@
},
{
"id":"bmd_to_bamrecompress",
"from":"bmd_tee3:__OUT1__",
"from":"bmd_target_multiway:__BAM_OUT__",
"to":"bamrecompress_target"
},
{
"id":"final_stretch",
"from":"bamrecompress_target",
"to":"target_bam"
},
##################################################
# check input primary/sequence data matches output
##################################################
{
"id":"phix_bam_to_bamcat",
"from":"phix_bam",
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