Skip to content

add optional stage1 methods to allow analysis using product crams as input (instead of default BCL) #331

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
dozy wants to merge 9 commits into
base: devel
Choose a base branch
from
Open

add optional stage1 methods to allow analysis using product crams as input (instead of default BCL) #331

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
9 commits
Select commit Hold shift + click to select a range
b3ad797
fix inheritance of undef parameter values bug
dozy Nov 21, 2023
e26eb64
allow initial input bam to be produced by "bambi i2b" or some alterna…
dozy Nov 21, 2023
53b340a
add reheader step
dozy Dec 5, 2023
07a046e
add -h flag (header SAM file) to samtools merge step
dozy Dec 6, 2023
98d8da2
give the reheader_rg_id parameter a default value (value of i2b_rg pa…
dozy Dec 6, 2023
b20b156
remove spurious --input-fmt flag from samtools merge command with BAM…
dozy Dec 6, 2023
289d636
add parameters to allow specification of sort order of input reads in…
dozy Dec 13, 2023
5b44301
add -T (temporary file prefix) flag to collate step
dozy Dec 15, 2023
8a50dc9
extend default list of preserved aux tags in reset command (now BC,QT…
dozy Dec 19, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 1 addition & 6 deletions bin/vtfp.pl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -678,18 +678,13 @@ sub fetch_param_entry {
}
}

my $candidate;
if(exists $param_entry->{_value}) {
$candidate = $param_entry; # already evaluated, return cached value (allowing undef)
return $param_entry; # already evaluated, return cached value (allowing undef)
}

push @{$aux->{irp}}, $param_name;
$retval = resolve_subst_constructor($param_name, $param_entry->{subst_constructor}, $params, $ewi, $aux);

if(not $retval and $candidate) {
$retval = $candidate->{_value};
}

if(defined $retval) {
$param_entry->{_value} = $retval;
}
Expand Down
119 changes: 119 additions & 0 deletions data/vtlib/bambi_i2b.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,119 @@
{
"version":"2.0",
"description":"This pipeline starts with Illumina2Bam, and ends by running SplitBamByReadGroup to create separate BAM files for each sample.",
"subgraph_io":{
"ports":{
"inputs":{},
"outputs":{
"_stdout_":"i2b"
}
}
},
"subst_params":[
{"id":"rpt","description":"Run/Position/TagIndex, though here it is generally only Run/Position. Used in defaults/constructors for i2b_rg,decoder_metrics,md5_file,seqchksum_file,spatial_filter_file and filtered_bam"},
{"id":"i2b_run_path","description":"path to runfolder. Provides a base on which i2b_runfolder_path can be constructed"},
{"id":"i2b_runfolder","description":"runfolder directory. Provides a base on which platform unit and i2b_runfolder_path can be constructed"},
{"id":"i2b_runfolder_path","description":"full path to runfolder. Provides a base on which platform unit, intensities directory and (indirectly) basecalls directories can be constructed",
"subst_constructor":{
"vals":[ {"subst":"i2b_run_path","required":"yes"}, {"subst":"i2b_runfolder","required":"yes"} ],
"postproc":{"op":"concat","pad":"/"}
}

},
{
"id":"i2b_intensity_dir",
"required":"yes",
"description":"Illumina intensities directory including config xml file, and clocs, locs or pos files under lane directory, using Data/Intensities directory under runfolder if not given",
"subst_constructor":{
"vals":[ {"subst":"i2b_runfolder_path","required":"yes"}, "/", {"subst":"i2b_data_intensities_dir_suffix","ifnull":"Data/Intensities"} ],
"postproc":{"op":"concat","pad":""}
}
},
{
"id":"i2b_basecalls_dir",
"required":"no",
"description":"Illumina basecalls directory including config xml file, and filter files, bcl, maybe scl files under lane cycle directory, using BaseCalls directory under intensities if not given.",
"subst_constructor":{
"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_basecalls_dir_suffix","ifnull":"BaseCalls"} ],
"postproc":{"op":"concat","pad":""}
}
},
{
"id":"i2b_bam_basecalls_dir",
"required":"no",
"description":"full path to the BAM_basecalls directory; a default parameter value for the tag_metrics qc check",
"subst_constructor":{
"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_bam_basecalls_dir_suffix","required":"yes"} ],
"postproc":{"op":"concat","pad":""}
}
},
{"id":"i2b_lane","required":"yes","comment":"Lane number"},
{
"id":"i2b_pu",
"description":"The platform unit, using runfolder name plus lane number if not given",
"subst_constructor":{
"vals":[ {"subst":"i2b_runfolder"}, "_", {"subst":"i2b_lane"} ],
"postproc":{"op":"concat","pad":""}
}
},
{"id":"i2b_library_name","description":"The name of the sequenced library"},
{"id":"i2b_rg", "description":"ID used to link RG header record with RG tag in SAM record", "default":{"subst":"rpt"}},
{"id":"i2b_bc_seq_val","required":"no","description":"Tag name for barcode sequence. Illumina2bam default is BC"},
{"id":"i2b_bc_qual_val","required":"no","description":"Tag name for barcode quality. Illumina2bam default is QT"},
{"id":"i2b_sec_bc_seq_val","required":"no","description":"Tag name for second barcode sequence. Illumina2bam default is null"},
{"id":"i2b_sec_bc_qual_val","required":"no","description":"Tag name for second barcode quality. Illumina2bam default is null"},
{"id":"i2b_study_name","description":"The name of the study"},
{
"id":"i2b_sample_aliases",
"default":"UNSPECIFIED",
"comment":"produces a comma-separated string from array of i2b_sample_alias values",
"subst_constructor":{
"vals":{"subst":"i2b_sample_alias", "ifnull":["UNSPEC"]},
"postproc":{"op":"concat","pad":","}
}
}
],
"nodes":[
{
"id":"i2b",
"type":"EXEC",
"description":"Create the initial BAM file from the data generated by the Illumina machine using bambi i2b",
"use_STDIN":false,
"use_STDOUT":true,
"cmd":[
"bambi",
"i2b",
{"subst":"i2b_intensity_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--intensity-dir", {"subst":"i2b_intensity_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_basecalls_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--basecalls-dir", {"subst":"i2b_basecalls_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_lane_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--lane", {"subst":"i2b_lane","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_pu_flag","ifnull":{"subst_constructor":{"vals":[ "--platform-unit", {"subst":"i2b_pu"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_rg_flag","ifnull":{"subst_constructor":{"vals":[ "--read-group-id", {"subst":"i2b_rg"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--barcode-tag", {"subst":"i2b_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--quality-tag", {"subst":"i2b_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_sec_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-barcode-tag", {"subst":"i2b_sec_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_sec_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-quality-tag", {"subst":"i2b_sec_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_tile_flag","ifnull":{"subst_constructor":{"vals":[ "--first-tile", {"subst":"i2b_first_tile"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_tile_limit_flag","ifnull":{"subst_constructor":{"vals":[ "--tile-limit", {"subst":"i2b_tile_limit"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_library_flag","ifnull":{"subst_constructor":{"vals":[ "--library-name", {"subst":"i2b_library_name"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_study_name_flag","ifnull":{"subst_constructor":{"vals":[ "--study-name", {"subst":"i2b_study_name"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_sample_alias_flag","ifnull":{"subst_constructor":{"vals":[ "--sample-alias", {"subst":"i2b_sample_aliases"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_bc_read_flag","ifnull":{"subst_constructor":{"vals":[ "--bc-read", {"subst":"i2b_bc_read"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_thread_count_flag","ifnull":{"subst_constructor":{"vals":[ "--threads", {"subst":"i2b_thread_count"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_tqlen_flag","ifnull":{"subst_constructor":{"vals":[ "--queue-len", {"subst":"i2b_tqlen"} ],"postproc":{"op":"concat","pad":"="}}}},
{"select":"i2b_nocall_qual_switch", "required":true, "select_range":[1], "default":"off", "cases":{ "on": "--nocall-quality", "off":[]}},
{"subst":"i2b_arbitrary_flags", "comment":"this allows arbitrary sets of flag strings to be inserted in the command" },
"--output-file=-",
"--compression-level=0"
]
}
],
"edges":[]
}
122 changes: 15 additions & 107 deletions data/vtlib/bcl2bam_phix_deplex_wtsi_stage1_template.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,117 +2,25 @@
"description":"This pipeline starts with Illumina2Bam, and ends by running SplitBamByReadGroup to create separate BAM files for each sample.",
"version":"2.0",
"subst_params":[
{"id":"rpt","description":"Run/Position/TagIndex, though here it is generally only Run/Position. Used in defaults/constructors for i2b_rg,decoder_metrics,md5_file,seqchksum_file,spatial_filter_file and filtered_bam"},
{"id":"i2b_run_path","description":"path to runfolder. Provides a base on which i2b_runfolder_path can be constructed"},
{"id":"i2b_runfolder","description":"runfolder directory. Provides a base on which platform unit and i2b_runfolder_path can be constructed"},
{"id":"i2b_runfolder_path","description":"full path to runfolder. Provides a base on which platform unit, intensities directory and (indirectly) basecalls directories can be constructed",
"subst_constructor":{
"vals":[ {"subst":"i2b_run_path","required":"yes"}, {"subst":"i2b_runfolder","required":"yes"} ],
"postproc":{"op":"concat","pad":"/"}
}

},
{
"id":"i2b_intensity_dir",
"required":"yes",
"description":"Illumina intensities directory including config xml file, and clocs, locs or pos files under lane directory, using Data/Intensities directory under runfolder if not given",
"subst_constructor":{
"vals":[ {"subst":"i2b_runfolder_path","required":"yes"}, "/", {"subst":"i2b_data_intensities_dir_suffix","ifnull":"Data/Intensities"} ],
"postproc":{"op":"concat","pad":""}
}
},
{
"id":"i2b_basecalls_dir",
"required":"no",
"description":"Illumina basecalls directory including config xml file, and filter files, bcl, maybe scl files under lane cycle directory, using BaseCalls directory under intensities if not given.",
"subst_constructor":{
"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_basecalls_dir_suffix","ifnull":"BaseCalls"} ],
"postproc":{"op":"concat","pad":""}
}
},
{
"id":"i2b_bam_basecalls_dir",
"required":"no",
"description":"full path to the BAM_basecalls directory; a default parameter value for the tag_metrics qc check",
"subst_constructor":{
"vals":[ {"subst":"i2b_intensity_dir","required":"yes"}, "/", {"subst":"i2b_bam_basecalls_dir_suffix","required":"yes"} ],
"postproc":{"op":"concat","pad":""}
}
},
{"id":"i2b_lane","required":"yes","comment":"Lane number"},
{
"id":"i2b_pu",
"description":"The platform unit, using runfolder name plus lane number if not given",
"subst_constructor":{
"vals":[ {"subst":"i2b_runfolder"}, "_", {"subst":"i2b_lane"} ],
"postproc":{"op":"concat","pad":""}
}
},
{"id":"i2b_library_name","description":"The name of the sequenced library"},
{"id":"i2b_rg", "description":"ID used to link RG header record with RG tag in SAM record", "default":{"subst":"rpt"}},
{"id":"i2b_bc_seq_val","required":"no","description":"Tag name for barcode sequence. Illumina2bam default is BC"},
{"id":"i2b_bc_qual_val","required":"no","description":"Tag name for barcode quality. Illumina2bam default is QT"},
{"id":"i2b_sec_bc_seq_val","required":"no","description":"Tag name for second barcode sequence. Illumina2bam default is null"},
{"id":"i2b_sec_bc_qual_val","required":"no","description":"Tag name for second barcode quality. Illumina2bam default is null"},
{"id":"i2b_study_name","description":"The name of the study"},
{
"id":"i2b_sample_aliases",
"default":"UNSPECIFIED",
"comment":"produces a comma-separated string from array of i2b_sample_alias values",
"subst_constructor":{
"vals":{"subst":"i2b_sample_alias", "ifnull":["UNSPEC"]},
"postproc":{"op":"concat","pad":","}
}
},
{"id":"s1_runfolder_path","required":"yes","default":{"subst":"i2b_runfolder_path"}, "comment":"Stage1 runfolder path"},
{"id":"s1_basecalls_dir","required":"yes","default":{"subst":"i2b_basecalls_dir"}, "comment":"Stage1 BAM_basecalls directory"},
{"id":"s1_lane","required":"yes","default":{"subst":"i2b_lane"}, "comment":"Stage1 lane number"},
{"id":"qc_check_id_run","required":"yes"},
{"id":"qc_check_position","required":"yes","default":{"subst":"i2b_lane"}},
{"id":"qc_check_qc_in_dir","required":"yes","default":{"subst_constructor":{"vals":[{"subst":"i2b_runfolder_path"}, "Data/Intensities", {"subst":"i2b_bam_basecalls_dir"}],"postproc":{"op":"concat","pad":"/"}}}},
{"id":"qc_check_position","required":"yes","default":{"subst":"s1_lane"}},
{"id":"qc_check_qc_in_dir","required":"yes","default":{"subst_constructor":{"vals":[{"subst":"s1_runfolder_path"}, "Data/Intensities", {"subst":"s1_bam_basecalls_dir"}],"postproc":{"op":"concat","pad":"/"}}}},
{"id":"qc_check_qc_out_dir","required":"yes","default":{"subst_constructor":{"vals":[{"subst":"qc_check_qc_in_dir"}, "no_cal/archive/qc"],"postproc":{"op":"concat","pad":"/"}}}},
{"id":"run_lane_label", "description":"label constructed from id_run and position", "default":{"subst_constructor":{"vals":[{"subst":"qc_check_id_run"}, "_", {"subst":"i2b_lane"}],"postproc":{"op":"concat","pad":""}}}},
{"id":"run_lane_label", "description":"label constructed from id_run and position", "default":{"subst_constructor":{"vals":[{"subst":"qc_check_id_run"}, "_", {"subst":"s1_lane"}],"postproc":{"op":"concat","pad":""}}}},
{"id":"s1_output_format", "description":"output format for deplexed reads (bam/cram/etc)", "default":"cram"}
],
"nodes":[
{
"id":"illumina2bam",
"type":"EXEC",
"use_STDIN":false,
"use_STDOUT":true,
"comment":"Actual executable used depends on the value of the 12b_implementation parameter: java - use illumina2bam (default); bambi - use new bambi i2b",
"cmd":[
"bambi",
"i2b",
{"subst":"i2b_intensity_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--intensity-dir", {"subst":"i2b_intensity_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_basecalls_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--basecalls-dir", {"subst":"i2b_basecalls_dir","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_lane_flag","required":true,"ifnull":{"subst_constructor":{"vals":[ "--lane", {"subst":"i2b_lane","required":true} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_pu_flag","ifnull":{"subst_constructor":{"vals":[ "--platform-unit", {"subst":"i2b_pu"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_rg_flag","ifnull":{"subst_constructor":{"vals":[ "--read-group-id", {"subst":"i2b_rg"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--barcode-tag", {"subst":"i2b_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--quality-tag", {"subst":"i2b_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_sec_bc_seq_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-barcode-tag", {"subst":"i2b_sec_bc_seq_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_sec_bc_qual_flag","ifnull":{"subst_constructor":{"vals":[ "--sec-quality-tag", {"subst":"i2b_sec_bc_qual_val"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_tile_flag","ifnull":{"subst_constructor":{"vals":[ "--first-tile", {"subst":"i2b_first_tile"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_tile_limit_flag","ifnull":{"subst_constructor":{"vals":[ "--tile-limit", {"subst":"i2b_tile_limit"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_library_flag","ifnull":{"subst_constructor":{"vals":[ "--library-name", {"subst":"i2b_library_name"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_study_name_flag","ifnull":{"subst_constructor":{"vals":[ "--study-name", {"subst":"i2b_study_name"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_sample_alias_flag","ifnull":{"subst_constructor":{"vals":[ "--sample-alias", {"subst":"i2b_sample_aliases"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_bc_read_flag","ifnull":{"subst_constructor":{"vals":[ "--bc-read", {"subst":"i2b_bc_read"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_index_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-index-cycle", {"subst":"i2b_first_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_index_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-index-cycle", {"subst":"i2b_final_index_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_0_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_0_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_0"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_first_1_flag","ifnull":{"subst_constructor":{"vals":[ "--first-cycle", {"subst":"i2b_first_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_final_1_flag","ifnull":{"subst_constructor":{"vals":[ "--final-cycle", {"subst":"i2b_final_1"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_thread_count_flag","ifnull":{"subst_constructor":{"vals":[ "--threads", {"subst":"i2b_thread_count"} ],"postproc":{"op":"concat","pad":"="}}}},
{"subst":"i2b_tqlen_flag","ifnull":{"subst_constructor":{"vals":[ "--queue-len", {"subst":"i2b_tqlen"} ],"postproc":{"op":"concat","pad":"="}}}},
{"select":"i2b_nocall_qual_switch", "required":true, "select_range":[1], "default":"off", "cases":{ "on": "--nocall-quality", "off":[]}},
{"subst":"i2b_arbitrary_flags", "comment":"this allows arbitrary sets of flag strings to be inserted in the command" },
"--output-file=-",
"--compression-level=0"
],
"description":"Create the initial BAM file from the data generated by the Illumina machine"
},
{
"id":"produce_init_bam",
"type":"VTFILE",
"comment":"inputs: _stdin_ (bam), reference; outputs: _stdout_ (bam)",
"node_prefix":"pib_",
"name":{"subst":"s1_produce_init_bam_method", "required":true, "ifnull":{"select":"i2b_switch", "default":"i2b", "select_range":[1], "cases":{"i2b":"bambi_i2b.json", "reanalysis":"pib_reanalysis.json"}}},
"description":"subgraph containing i2b or reanalysis initialisation"
},
{
"id":"tee_i2b",
"type":"EXEC",
Expand Down Expand Up @@ -435,7 +343,7 @@
}
],
"edges":[
{ "id":"illumina2bam_to_ti2b", "from":"illumina2bam", "to":"tee_i2b" },
{ "id":"illumina2bam_to_ti2b", "from":"produce_init_bam", "to":"tee_i2b" },
{ "id":"ti2b_to_bamadapterfind", "from":"tee_i2b:baf", "to":"bamindexdecoder" },
{ "id":"decoder_to_metrics", "from":"bamindexdecoder:metrics_file", "to":"decoder_metrics" },
{ "id":"decoder_metrics_to_qc_tag_metrics", "from":"decoder_metrics", "to":"qc_tag_metrics_check" },
Expand Down
Loading