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add static parameter files for stage2 reanalysis
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improve naming of template names and parameter names&values for stage2 input preprocessing
dozy committed Aug 28, 2024
1 parent ec6c748 commit b4c6065
Showing 5 changed files with 86 additions and 2 deletions.
13 changes: 13 additions & 0 deletions data/static_params/stage2_reanalysis/align_bwa_mem2.json
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@@ -0,0 +1,13 @@
{
"assign": [
{
"alignment_method": "bwa_mem",
"bwa_executable": "bwa-mem2"
}
],
"assign_local": {},
"ops": {
"splice": [],
"prune": []
}
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,37 @@
{
"assign": [
{
"spatial_filter_switch":"off",
"markdup_optical_distance_value": "100",
"s2_se_pe": "pe",
"samtools_executable": "samtools",
"s2_input_format": "cram",
"markdup_method": "duplexseq",
"s2_ppi_switch":"s2_ppi",
"pp_read2tags":"on",
"pp_import_method":"crammerge",
"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",
"realignment_switch":1
}
],
"assign_local": {},
"ops": {
"splice": [
"aln_bam12auxmerge:-foptgt_000_fixmate:",
"foptgt_seqchksum_file:-scs_cmp_seqchksum:outputchk"
],
"prune": [
"foptgt.*_bmd_multiway:calibration_pu-",
"foptgt_cram_tee:c2a-",
"foptgt.*samtools_stats_F0.*_target.*-",
"foptgt.*samtools_stats_F0.*00_bait.*-",
"aln_tee3_tee3:to_phix_aln-scs_cmp_seqchksum:outputchk",
"ssfqc_tee_ssfqc:subsample-"
]
}
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,35 @@
{
"assign": [
{
"spatial_filter_switch":"off",
"markdup_optical_distance_value": "100",
"s2_se_pe": "pe",
"samtools_executable": "samtools",
"s2_input_format": "cram",
"markdup_method": "duplexseq",
"s2_ppi_switch":"s2_ppi",
"pp_read2tags":"on",
"pp_import_method":"fastq",
"incrams": "DUMMY",
"s2_filter_files": "DUMMY",
"spatial_filter_file": "DUMMY",
"phix_reference_genome_fasta":"DUMMY",
"realignment_switch":1
}
],
"assign_local": {},
"ops": {
"splice": [
"aln_bam12auxmerge:-foptgt_000_fixmate:",
"foptgt_seqchksum_file:-scs_cmp_seqchksum:outputchk"
],
"prune": [
"foptgt.*_bmd_multiway:calibration_pu-",
"foptgt_cram_tee:c2a-",
"foptgt.*samtools_stats_F0.*_target.*-",
"foptgt.*samtools_stats_F0.*00_bait.*-",
"aln_tee3_tee3:to_phix_aln-scs_cmp_seqchksum:outputchk",
"ssfqc_tee_ssfqc:subsample-"
]
}
}
3 changes: 1 addition & 2 deletions data/vtlib/alignment_wtsi_stage2_template.json
Original file line number Diff line number Diff line change
@@ -102,8 +102,7 @@
"select":"s2_ppi_switch", "default":"crammerge","select_range":[1],
"cases":{
"crammerge":"crammerge.json",
"pp_ns":"fastq_s2_pi.json",
"aviti":"elembio_nanoseq_s2_pi.json"
"s2_ppi":"stage2_preprocess_inputs.json"
}
}},
"subst_map":{"input_format":{"subst":"s2_input_format"}},
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