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add FASTQ input option to non-consented human split analysis #357

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merged 3 commits into from
Oct 24, 2024
Merged

add FASTQ input option to non-consented human split analysis #357

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d4e910c
add FASTQ input option to non-consented human split analysis
dozy Oct 17, 2024
c3bafdc
add static parameters file for container nchs reanalysis with FASTQ i…
dozy Oct 18, 2024
3da2e02
add dummy value for incrams parameter when using FASTQ input
dozy Oct 22, 2024
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36 changes: 36 additions & 0 deletions data/static_params/stage2_reanalysis/base_params_samtools_nchs_fastq.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,36 @@
{
"assign": [
{
"spatial_filter_switch":"off",
"markdup_optical_distance_value": "100",
"s2_se_pe": "pe",
"samtools_executable": "samtools",
"s2_input_format": "cram",
"markdup_method": "samtools",
"s2_ppi_switch":"s2_ppi",
"pp_read2tags":"off",
"pp_import_method":"fastq",
"fastq_s2_pi_fq1": "DUMMY",
"fastq_s2_pi_fq2": "DUMMY",
"fastq_s2_pi_RG_ID": "DUMMY",
"s2_filter_files": "DUMMY",
"spatial_filter_file": "DUMMY",
"phix_reference_genome_fasta":"DUMMY",
"incrams": "DUMMY",
"realignment_switch":0
}
],
"assign_local": {},
"ops": {
"splice": [],
"prune": [
"fop[ht].*_bmd_multiway:calibration_pu-",
"foptgt_cram_tee:c2a-",
"fop[ht].*samtools_stats_F0.*_target.*-",
"fop[ht].*samtools_stats_F0.*00_bait.*-",
"aln_tee4_tee4:to_phix_aln-alignment_filter:phix_bam_in",
"alignment_filter:phix_bam_out-scs_merge_output_seqchksum:__PHIX_CHKSUM_IN__",
"ssfqc_tee_ssfqc:subsample-"
]
}
}
35 changes: 14 additions & 21 deletions data/vtlib/alignment_wtsi_stage2_humansplit_template.json
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,6 @@
"required": "no",
"comment":"this will expand to a set of subst_param elements"
},

{
"id":"spatial_filter_rg_flag",
"required":"no",
Expand Down Expand Up @@ -113,24 +112,20 @@
],
"nodes":[
{
"id":"crammerge",
"type":"EXEC",
"use_STDIN": false,
"use_STDOUT": true,
"cmd": [
"samtools",
"merge",
"-n",
"-O", "BAM",
"-l", "0",
{"select":"s2_input_format", "default":"cram", "select_range":[1], "cases":{
"cram":["--input-fmt-option", "no_ref=1"],
"bam":["--input-fmt", "bam"]
"id":"preprocess_inputs",
"type":"VTFILE",
"name":{"subst":"s2_preprocess_inputs_method", "required":true,
"ifnull":{
"select":"s2_ppi_switch", "default":"crammerge","select_range":[1],
"cases":{
"crammerge":"crammerge.json",
"s2_ppi":"stage2_preprocess_inputs.json"
}
}},
"-",
{"subst":"incrams"}
],
"description":"merge individual cram files from a sample into one cram file"
"subst_map":{"input_format":{"subst":"s2_input_format"}},
"comment":"inputs: NONE; outputs: _stdout_ (bam), subst_map_parameters:[input_format]",
"node_prefix":"ppi_",
"description":"subgraph to preprocess inputs. Default: merge individual cram files from a sample into one bam file"
},
{
"id":"spatial_filter",
Expand Down Expand Up @@ -172,7 +167,6 @@
"name":{"subst":"subsample_vtf", "ifnull":"subsample.json"},
"description":""
},

{
"id":"haplotag",
"description":"haplotagging post-processing",
Expand All @@ -190,7 +184,6 @@
"node_prefix":{ "subst_constructor":{ "vals": [ "ht_", {"subst":"phix_or_target", "ifnull":"pot"}, "_" ], "postproc":{"op":"concat", "pad":""} } },
"name":"haplotagging.json"
},

{
"id":"target_alignment",
"type":"VTFILE",
Expand Down Expand Up @@ -297,7 +290,7 @@
}
],
"edges":[
{ "id":"src_to_bc2", "from":"crammerge", "to":{"subst":"post_cm","required":true} },
{ "id":"src_to_bc2", "from":"preprocess_inputs", "to":{"subst":"post_cm","required":true} },
{"select":"spatial_filter_switch", "required":true, "select_range":[1], "default":"on", "allow_unspec_keys":true,
"cases":{
"on": [
Expand Down
5 changes: 2 additions & 3 deletions data/vtlib/alignment_wtsi_stage2_template.json
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Original file line number Diff line number Diff line change
Expand Up @@ -17,14 +17,12 @@
"required": "no",
"comment":"this will expand to a set of subst_param elements"
},

{
"id":"spatial_filter_rg_flag",
"required":"no",
"comment":"flag will disappear unless RG values are given (for multiple filter file application)",
"subst_constructor":{ "vals":[ "--rg", {"subst":"spatial_filter_rg_value"} ] }
},

{"id":"af_metrics_name","required":"no","default":"alignment_filter_metrics.json"},
{
"id":"af_metrics",
Expand Down Expand Up @@ -146,7 +144,8 @@
{
"id":"spatial_filter_stats",
"type":"OUTFILE",
"name":{"subst":"spatial_filter_stats", "required":true, "ifnull":{"subst_constructor":{"vals":[ {"subst":"outdatadir"}, "/", {"subst":"rpt"}, ".spatial_filter.stats" ], "postproc":{"op":"concat","pad":""}}}} },
"name":{"subst":"spatial_filter_stats", "required":true, "ifnull":{"subst_constructor":{"vals":[ {"subst":"outdatadir"}, "/", {"subst":"rpt"}, ".spatial_filter.stats" ], "postproc":{"op":"concat","pad":""}}}}
},
{
"id":"subsample_fqc",
"type":"VTFILE",
Expand Down