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added fixmates, calibrartion_pu, adddupmarksupport and bamstreamingma…
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…rkduplicates to current production tophat2 template
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@dozy
dozy committed Oct 14, 2014
1 parent aa73fc8 commit 4731464
Showing 1 changed file with 91 additions and 96 deletions.
187 changes: 91 additions & 96 deletions data/tophat2_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 RNASeq 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": true,
"cmd":"tee __pFIFO0__"
},
{
"id":"bmd_tee1",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"tee __FIFO1__"
},
{
"id":"bmd_tee2",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"tee __FIFO2__"
},
{
"id":"bmd_tee3",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"tee __FIFO3__"
},
{
"id":"bmd_phix_tee1",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"tee __pFIFO1__"
"use_STDOUT": false,
"cmd":"teepot -w 300 __SCRAMBLE_OUT__ __BAMCHECK_OUT__ __FLAGSTAT_OUT__ __CALIBRATION_PU_OUT__ __BAM_OUT__"
},
{
"id":"bmd_phix_tee2",
"id":"bmd_target_multiway",
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"tee __pFIFO2__"
"use_STDOUT": false,
"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 @@ -665,7 +697,7 @@
"type":"EXEC",
"use_STDIN": true,
"use_STDOUT": true,
"cmd":"bamsort SO=queryname level=0"
"cmd":"bamsort level=0 verbose=0 SO=queryname"
},
{
"id":"bamreset_prealn",
Expand All @@ -689,9 +721,6 @@
"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 @@ -747,15 +776,12 @@
}
}
},
#######################
# 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 @@ -766,7 +792,7 @@
"required":"yes",
"subst_constructor":{
"vals":[
"bammarkduplicates ",
"bamstreamingmarkduplicates ",
"level=0 ",
"M=",
{"subst_param_name":"outdatadir","required":"no","default":"."},
Expand Down Expand Up @@ -820,15 +846,12 @@
}
}
},
#############################
# 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 @@ -839,7 +862,7 @@
"required":"yes",
"subst_constructor":{
"vals":[
"bammarkduplicates ",
"bamstreamingmarkduplicates ",
"level=0 ",
"M=",
{"subst_param_name":"outdatadir","required":"no","default":"."},
Expand Down Expand Up @@ -892,9 +915,6 @@
}
}
},
##################################################
# check input primary/sequence data matches output
##################################################
{
"id":"bamcat_output",
"type":"EXEC",
Expand Down Expand Up @@ -939,68 +959,58 @@
{
"id":"bammarkduplicates_phix_to_tee",
"from":"bammarkduplicates_phix",
"to":"bmd_phix_tee0"
},
{
"id":"bmd_phix_tee0_to_bmd_phix_tee0",
"from":"bmd_phix_tee0:__pFIFO0__",
"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:__pFIFO1__",
"from":"bmd_phix_multiway:__SCRAMBLE_OUT__",
"to":"scramble_phix"
},
{
"id":"tee_to_scramble",
"from":"bmd_tee1:__FIFO1__",
"from":"bmd_target_multiway:__SCRAMBLE_OUT__",
"to":"scramble"
},
{
"id":"bmd_phix_tee1_to_bmd_phix_tee2",
"from":"bmd_phix_tee1",
"to":"bmd_phix_tee2"
},
{
"id":"bmd_tee1_to_bmd_tee2",
"from":"bmd_tee1",
"to":"bmd_tee2"
},
{
"id":"tee_phix_to_bamcheck_phix",
"from":"bmd_phix_tee2",
"from":"bmd_phix_multiway:__BAMCHECK_OUT__",
"to":"bamcheck_phix"
},
{
"id":"tee_to_bamcheck",
"from":"bmd_tee2:__FIFO2__",
"from":"bmd_target_multiway:__BAMCHECK_OUT__",
"to":"bamcheck"
},
{
"id":"bmd_tee2_to_bmd_tee3",
"from":"bmd_tee2",
"to":"bmd_tee3"
},
{
"id":"bmd_tee2_phix_to_flagstat",
"from":"bmd_phix_tee2:__pFIFO2__",
"from":"bmd_phix_multiway:__FLAGSTAT_OUT__",
"to":"flagstat_phix"
},
{
"id":"bmd_tee3_to_flagstat_filter",
"from":"bmd_tee3:__FIFO3__",
"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 @@ -1056,9 +1066,6 @@
"from":"bamrecompress_input",
"to":"int_adp_bam"
},
############################################################
# tophat alignment
############################################################
{
"id":"ti_to_bamcollate2_ranking",
"from":"tee_input:__FIFO__",
Expand Down Expand Up @@ -1187,9 +1194,6 @@
{
"id":"bam12auxmerge_to_alignment_filter",
"from":"bam12auxmerge",
#################
# AlignmentFilter
#################
"to":"alignment_filter:__TARGET_INBAM__"
},
{
Expand All @@ -1202,9 +1206,6 @@
"from":"alignment_filter:__AF_METRICS__",
"to":"af_metrics"
},
#####################
# phiX BAM production
#####################
{
"id":"alignmentfilter_to_bamsort_coord_phix",
"from":"alignment_filter:__PHIX_OUTBAM__",
Expand All @@ -1217,17 +1218,14 @@
},
{
"id":"bmd_phix_tee0_to_bamrecompress_phix",
"from":"bmd_phix_tee0",
"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 @@ -1240,17 +1238,14 @@
},
{
"id":"bmd_to_bamrecompress",
"from":"bmd_tee3",
"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",
Expand Down

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