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Merge pull request #349 from dozy/stage2_init_options
Stage2 init options
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| { | ||
| "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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| 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":0 | ||
| } | ||
| ], | ||
| "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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| 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":0 | ||
| } | ||
| ], | ||
| "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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| { | ||
| "version":"2.0", | ||
| "description":"run bwa mem to to align input bam to supplied reference genome", | ||
| "subgraph_io":{ | ||
| "ports":{ | ||
| "inputs":{ | ||
| }, | ||
| "outputs":{ | ||
| "_stdout_":"crammerge" | ||
| } | ||
| } | ||
| }, | ||
| "subst_params":[], | ||
| "nodes":[ | ||
| { | ||
| "id":"crammerge", | ||
| "type":"EXEC", | ||
| "use_STDIN": false, | ||
| "use_STDOUT": true, | ||
| "cmd": [ | ||
| "samtools", | ||
| "merge", | ||
| "-n", | ||
| "-O", "BAM", | ||
| "-l", "0", | ||
| {"select":"input_format", "default":"cram", "select_range":[1], "cases":{ | ||
| "cram":["--input-fmt-option", "no_ref=1"], | ||
| "bam":["--input-fmt", "bam"] | ||
| }}, | ||
| "-", | ||
| {"subst":"incrams", "required":true} | ||
| ], | ||
| "description":"merge individual cram files from a sample into one bam file" | ||
| } | ||
| ], | ||
| "edges":[] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,54 @@ | ||
| { | ||
| "version":"2.0", | ||
| "description":"read2tags for NanoSeq processing, including preparatory collation and reset", | ||
| "subgraph_io":{ | ||
| "ports":{ | ||
| "inputs":{"_stdin_":"collate"}, | ||
| "outputs":{ "_stdout_":"read2tags" } | ||
| } | ||
| }, | ||
| "nodes":[ | ||
| { | ||
| "id":"collate", | ||
| "type": "EXEC", | ||
| "use_STDIN": true, | ||
| "use_STDOUT": true, | ||
| "cmd": [ | ||
| {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "collate", | ||
| "--threads", {"subst":"s2_r2t_coll_threads","required":true,"ifnull":2}, | ||
| "-u", | ||
| "-O", | ||
| "-" | ||
| ] | ||
| }, | ||
| { | ||
| "id":"reset", | ||
| "type": "EXEC", | ||
| "use_STDIN": true, | ||
| "use_STDOUT": true, | ||
| "cmd": [ | ||
| {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "reset", | ||
| "--threads", {"subst":"s2_r2t_rs_threads","required":true,"ifnull":4}, | ||
| "--output-fmt", "BAM,level=0" | ||
| ] | ||
| }, | ||
| { | ||
| "id":"read2tags", | ||
| "type": "EXEC", | ||
| "use_STDIN": true, | ||
| "use_STDOUT": true, | ||
| "cmd": [ | ||
| {"subst":"bambi_executable", "required":true, "ifnull":"bambi"}, "read2tags", | ||
| "--tags", "rb,mb,br,rb,mb,br", | ||
| "--qtags", "rq,mq,bq,rq,mq,bq", | ||
| "--positions", "1:1:1:3,1:2:1:3,1:1:4:7,2:2:1:3,2:1:1:3,2:2:4:7", | ||
| "--compression-level", 0, | ||
| "--output-fmt", "bam" | ||
| ] | ||
| } | ||
| ], | ||
| "edges":[ | ||
| { "id":"collate_to_reset", "from":"collate","to":"reset" }, | ||
| { "id":"reset_to_read2tags", "from":"reset", "to":"read2tags" } | ||
| ] | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| { | ||
| "version":"2.0", | ||
| "description":"alternate pre-processing method for stage2 inputs accepting FASTQ input (for e.g. Elembio NanoSeq)", | ||
| "subgraph_io":{ | ||
| "ports":{ | ||
| "inputs":{}, | ||
| "outputs":{ "_stdout_": | ||
| {"select":"pp_read2tags", "required":true, "default":"off", | ||
| "cases":{ | ||
| "off": "import", | ||
| "on": "read2tags" | ||
| } | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "nodes":[ | ||
| { | ||
| "id":"import", | ||
| "type":"EXEC", | ||
| "use_STDIN": false, | ||
| "use_STDOUT": true, | ||
| "cmd": { | ||
| "select":"pp_import_method", | ||
| "required":true, | ||
| "select_range":[1], | ||
| "default":"crammerge", | ||
| "cases":{ | ||
| "crammerge": | ||
| [ | ||
| {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "merge", | ||
| "-n", | ||
| "-O", "BAM", | ||
| "-l", "0", | ||
| {"select":"input_format", "default":"cram", "select_range":[1], "cases":{ | ||
| "cram":["--input-fmt-option", "no_ref=1"], | ||
| "bam":["--input-fmt", "bam"] | ||
| }}, | ||
| "-", | ||
| {"subst":"incrams", "required":true} | ||
| ], | ||
| "fastq": | ||
| [ | ||
| {"subst":"samtools_executable", "required":true, "ifnull":"samtools"}, "import", | ||
| "-R", {"subst":"fastq_s2_pi_RG_ID","required":true, "comment":"readgroup"}, | ||
| "-1", {"subst":"fastq_s2_pi_fq1","required":true, "comment":"FASTQ read 1"}, | ||
| "-2", {"subst":"fastq_s2_pi_fq2","required":true, "comment":"FASTQ read 2"}, | ||
| {"select":"parse_casava_id", "default":"on", "select_range":[1], "cases":{ "on":["-i"], "off":[] }}, | ||
| {"subst":"parse_import_tags_flag", "ifnull":["-T", {"subst":"parse_import_tags","required":true,"ifnull":"*"}]}, | ||
| "-u", | ||
| "-O", "bam" | ||
| ] | ||
| } | ||
| } | ||
| }, | ||
| { | ||
| "id":"read2tags", | ||
| "type":{ | ||
| "select":"pp_read2tags", | ||
| "required":true, | ||
| "select_range":[1], | ||
| "default":"off", | ||
| "cases":{ | ||
| "on":"VTFILE", | ||
| "off":"INACTIVE" | ||
| } | ||
| }, | ||
| "use_STDIN": true, | ||
| "use_STDOUT": true, | ||
| "name":"read2tags.json", | ||
| "node_prefix":"r2t_" | ||
| } | ||
| ], | ||
| "edges":[ | ||
| {"select":"pp_read2tags", "required":true, "default":"off", "cases":{ | ||
| "off": [], | ||
| "on": [ { "id":"import_to_read2tags", "from":"import", "to":"read2tags" }] | ||
| } | ||
| } | ||
| ] | ||
| } |
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