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add static parameter files for stage2 reanalysis
improve naming of template names and parameter names&values for stage2 input preprocessing
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{ | ||
"assign": [ | ||
{ | ||
"alignment_method": "bwa_mem", | ||
"bwa_executable": "bwa-mem2" | ||
} | ||
], | ||
"assign_local": {}, | ||
"ops": { | ||
"splice": [], | ||
"prune": [] | ||
} | ||
} |
37 changes: 37 additions & 0 deletions
37
data/static_params/stage2_reanalysis/base_params_duplexseq_cram.json
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{ | ||
"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-" | ||
] | ||
} | ||
} |
35 changes: 35 additions & 0 deletions
35
data/static_params/stage2_reanalysis/base_params_duplexseq_fastq.json
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@@ -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-" | ||
] | ||
} | ||
} |
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