Seperated out the params into logical sections
This commit is contained in:
Neil Horner
parent
4782a1473c
commit
76fd8f9c81
@ -6,7 +6,7 @@ channels:
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- defaults
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dependencies:
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- python==3.8.*
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- aplanat >=0.5.0
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- aplanat >=0.6.2
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- epi2melabs
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- minimap2 ==2.24
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- samtools ==1.14
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@ -37,24 +37,29 @@
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"description": "Use additional heuristics to identify barcodes from file paths.",
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"help_text": "Enabling this option will group together files into samples by the presence of strings of the form `barcodeXXX` present in filenames, rather than simply files grouped into directories (as output by MinKNOW and the Guppy basecaller)."
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},
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"plot_gffcmp_stats": {
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"type": "boolean",
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"description": "Create a pdf of plots from showing gffcompare results"
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},
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"gffcompare_opts": {
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"type": "string",
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"description": "Extra options for gffcompare -r",
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"default": " -R "
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},
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"ref_genome": {
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"type": "string",
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"format": "file-path",
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"description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]"
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"description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]. Required for reference-based workflow"
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},
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"ref_annotation": {
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"type": "string",
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"format": "file-path",
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"description": "A reference annotation of gff format"
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}
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},
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"required": [
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"fastq"
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]
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},
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"global_options": {
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"title": "Global options",
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"type": "object",
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"description": "Options for both sub-workflows",
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"properties": {
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"threads": {
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"type": "integer",
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"default": 4
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},
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"use_pychopper": {
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"type": "boolean",
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@ -66,52 +71,15 @@
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"description": "Extra pychopper opts",
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"default": "-m edlib"
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},
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"threads": {
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"type": "integer",
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"default": 8
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},
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"minimap_index_opts": {
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"type": "string",
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"description": "minimap2 extra indexing options.",
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"default": "-k14"
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},
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"minimap2_opts": {
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"type": "string",
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"description": "minimap2 extra mapping options.",
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"default": "-uf"
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},
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"minimum_mapping_quality": {
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"type": "integer",
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"description": "filter aligned reads by MAPQ quality.",
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"default": 40
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},
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"poly_context": {
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"type": "integer",
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"description": "Region size at end of reads to apply poly(A) filter.",
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"default": 24
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},
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"max_poly_run": {
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"type": "integer",
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"description": "Max poly(A) region allowed with poly_context-sized end regions.",
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"default": 8
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},
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"bundle_min_reads": {
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"type": "integer",
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"description": "Minimum size of bam bundle for parallel processing."
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},
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"use_guide_annotation": {
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"type": "boolean",
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"description": "Use reference annotation in stringtie transcript assembly.",
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"default": "true"
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},
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"stringtie_opts": {
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"type": "string",
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"description": "Extra options for stringtie transcript assembly.",
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"default": " --conservative "
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},
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"disable_ping": {
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"type": "boolean"
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},
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"transcript_table_cov_thresh": {
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"type": "integer",
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"description": "Minimum coverage for a transcript to appear in the report table",
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@ -121,86 +89,132 @@
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"type": "boolean",
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"description": "Use denovo transcript assembly rather than reference guided",
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"default": false
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},
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"batch_size": {
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"type": "integer",
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"description": "Maximum sequences per input batch (-1 means no limit)",
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"default": -1
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},
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"batch_max_seq": {
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"type": "integer",
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"description": "Maximum sequences per input batch (-1 means no limit)",
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"default": -1
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},
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"cls_mode": {
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"type": "string",
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"description": "Clustering mode",
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"default": "sahlin"
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},
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"kmer_size": {
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"type": "integer",
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"description": "Kmer size",
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"default": 11
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},
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"window_size": {
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"type": "integer",
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"description": "Window size",
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"default": 15
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},
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"min_left_cls": {
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"type": "integer",
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"description": "Minimum cluser size in the left batch",
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"default": 2
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},
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"consensus_period": {
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"type": "integer",
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"description": "Consensus period (-1 means no consensus)",
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"default": 500
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},
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"consensus_minimum": {
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"type": "integer",
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"description": "Minimum consensus sample size:",
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"default": 50
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},
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"consensus_maximum": {
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"type": "integer",
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"description": "Maximum consensus sample size",
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"default": -150
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},
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"min_shared": {
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"type": "integer",
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"description": "Minimum number of minimizers shared between read and cluster",
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"default": 5
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},
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"min_qual": {
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"description": "Minimum average quality value",
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"type": "number",
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"default": 7.0
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},
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"mapped_threshold": {
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"description": "Minimum mapped fraction of read to be included in cluster",
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"type": "number",
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"default": 0.65
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},
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"aligned_threshold": {
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"tpye": "number",
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"description": "Minimum aligned fraction of read to be included in cluster",
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"default": 0.2
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},
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"min_fraction": {
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"type": "number",
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"description": "Minimum fraction of minimizers shared compared to best hit, in order to continue mapping",
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"default": 0.8
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},
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"min_prob_no_hits" : {
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"type": "number",
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"description": "Minimum probability for i consecutive minimizers to be different between read and representative",
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"default": 0.2
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}
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}
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},
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"reference_wf_options": {
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"title": "Options for reference-based workflow",
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"type": "object",
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"description": "Parameters that are used solely for the referenc-guided workflow",
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"properties": {
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"plot_gffcmp_stats": {
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"type": "boolean",
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"description": "Create a pdf of plots from showing gffcompare results"
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},
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"gffcompare_opts": {
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"type": "string",
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"description": "Extra options for gffcompare -r",
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"default": " -R "
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},
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"minimap_index_opts": {
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"type": "string",
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"description": "minimap2 extra indexing options.",
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"default": "-k14"
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},
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"minimap2_opts": {
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"type": "string",
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"description": "minimap2 extra mapping options.",
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"default": "-uf"
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},
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"minimum_mapping_quality": {
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"type": "integer",
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"description": "filter aligned reads by MAPQ quality.",
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"default": 40
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},
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"poly_context": {
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"type": "integer",
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"description": "Region size at end of reads to apply poly(A) filter.",
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"default": 24
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},
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"max_poly_run": {
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"type": "integer",
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"description": "Max poly(A) region allowed with poly_context-sized end regions.",
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"default": 8
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}
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}
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},
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"required": [
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"fastq"
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]
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"denovo_wf_options": {
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"title": "Options for de novo-based workflow",
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"type": "object",
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"description": "Parameters that are used solely for the de novo workflow",
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"properties": {
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"batch_size": {
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"type": "integer",
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"description": "Maximum sequences per input batch (-1 means no limit)",
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"default": -1
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},
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"batch_max_seq": {
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"type": "integer",
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"description": "Maximum sequences per input batch (-1 means no limit)",
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"default": -1
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},
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"cls_mode": {
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"type": "string",
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"description": "Clustering mode",
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"default": "sahlin"
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},
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"kmer_size": {
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"type": "integer",
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"description": "Kmer size",
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"default": 11
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},
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"window_size": {
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"type": "integer",
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"description": "Window size",
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"default": 15
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},
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"min_left_cls": {
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"type": "integer",
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"description": "Minimum cluser size in the left batch",
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"default": 2
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},
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"consensus_period": {
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"type": "integer",
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"description": "Consensus period (-1 means no consensus)",
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"default": 500
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},
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"consensus_minimum": {
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"type": "integer",
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"description": "Minimum consensus sample size:",
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"default": 50
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},
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"consensus_maximum": {
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"type": "integer",
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"description": "Maximum consensus sample size",
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"default": -150
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},
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"min_shared": {
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"type": "integer",
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"description": "Minimum number of minimizers shared between read and cluster",
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"default": 5
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},
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"min_qual": {
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"description": "Minimum average quality value",
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"type": "number",
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"default": 7.0
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},
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"mapped_threshold": {
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"description": "Minimum mapped fraction of read to be included in cluster",
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"type": "number",
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"default": 0.65
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},
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"aligned_threshold": {
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"tpye": "number",
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"description": "Minimum aligned fraction of read to be included in cluster",
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"default": 0.2
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},
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"min_fraction": {
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"type": "number",
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"description": "Minimum fraction of minimizers shared compared to best hit, in order to continue mapping",
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"default": 0.8
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},
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"min_prob_no_hits" : {
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"type": "number",
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"description": "Minimum probability for i consecutive minimizers to be different between read and representative",
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"default": 0.2
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}
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}
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},
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"meta_data": {
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"title": "Meta Data",
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@ -212,6 +226,12 @@
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"type": "string",
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"default": "report",
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"description": "Output report filename suffix."
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},
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"disable_ping": {
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"type": "boolean",
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"default": false,
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"description": "Enable to prevent sending a workflow ping."
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}
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}
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},
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@ -231,10 +251,20 @@
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/definitions/basic_input_output_options"
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},
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{
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"$ref": "#/definitions/global_options"
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},
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{
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"$ref": "#/definitions/reference_wf_options"
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},
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{
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"$ref": "#/definitions/denovo_wf_options"
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},
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{
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"$ref": "#/definitions/meta_data"
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},
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@ -253,7 +283,7 @@
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},
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"wfversion": {
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"type": "string",
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"default": "v0.1.0",
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"default": "v0.1.1",
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"hidden": true
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},
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"monochrome_logs": {
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