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110 lines (98 loc) · 5.62 KB
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Copy pathparams.json
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110 lines (98 loc) · 5.62 KB
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{
"_comment": "Copy this file, fill in your genome paths, and pass it with: nextflow run main.nf -params-file my_params.json",
"//1": "── Input / Output + Mandatory inputs ──────────────────────────────────────────────────────",
"input_dir": null,
"output_dir": null,
"genome": null,
"annotation": null,
"splice_scores_dir": null,
"repeats": null,
"prefix": null,
"//1a": "── Checkpoints (--from alignment|polish|bigbed) ─────────────────────────────────",
"from": null,
"bam_dir": null,
"polish_path": null,
"//1b": "── Checkpoint: start from bigbed step (skip metassembly + polishing) ─────────────────────",
"all_bed_path": null,
"//2": "── Linting [optional] ──────────────────────────────────",
"fq_skip_linting_at_start": false,
"fq_skip_linting_after_trimming": true,
"fq_skip_linting_after_deacon": true,
"//3": "── Decontamination [optional] ───────────────────────────────────────────",
"deacon_index_path": null,
"deacon_download_index": false,
"deacon_make_single_index": true,
"deacon_single_index_use_background": true,
"//4": "── Alignment [optional] ──────────────────────────────────",
"aligner": "STAR",
"star_index_path": null,
"star_ignore_gtf_for_index": false,
"star_ignore_gtf_for_mapping": true,
"star_twopass_junctions_file": null,
"//4a": "── CBQ reads [optional; encode_before_alignment requires aligner=ruSTAR] ─",
"bqtools_encode_fastqs": false,
"bqtools_encode_before_alignment": false,
"bqc_min_length": 15,
"bqc_quality_tail": 15,
"bqc_adapter_auto_detect": true,
"infer_strandedness": true,
"strand_transcriptome": null,
"strand_salmon_index": null,
"//5": "── Assembly [optional] ──────────────────────────────────",
"skip_assembly": false,
"assembly_by_chr": true,
"assembly_exclude_chromosomes": [],
"transmeta_use_annotation": true,
"assembler": "aletsch",
"metassembler": "beaver",
"aletsch_fallback_insert_size": null,
"aletsch_fallback_insert_std": 10,
"stringtie3_enable_nascent_assembly": false,
"stringtie3_include_nascent_rna": false,
"//5a": "── Polishing [optional] ──────────────────────────────────",
"do_twopass_polish": false,
"//5aa": "── ANNEVO annotation [optional] ──────────────────────────────────────────",
"annevo_annotation": null,
"annevo_predict": false,
"annevo_lineage": null,
"annevo_scatter": "chromosome",
"annevo_bins": 8,
"annevo_overlap_pred": null,
"//5ab": "── TIBERIUS annotation [optional] ────────────────────────────────────────",
"tiberius_annotation": null,
"tiberius_predict": false,
"tiberius_model_cfg": null,
"tiberius_scatter": "chromosome",
"tiberius_bins": 8,
"tiberius_batch_size": null,
"tiberius_seq_len": null,
"tiberius_protseq": false,
"tiberius_codingseq": false,
"tiberius_extra_args": "",
"//5b": "── ORF calling [optional] ────────────────────────────────────────────────",
"xorf_call_orfs": true,
"xorf_esm": false,
"xorf_esmfold_local_weights": null,
"xorf_selenocysteine_sites": null,
"xorf_custom_database": null,
"xorf_chunk_size": 20,
"xorf_skip_netstart": true,
"xorf_skip_transaid": false,
"xorf_predict_min_score_max_predictions": -1,
"xorf_predict_max_predictions": 3,
"xorf_predict_threshold": -1,
"xorf_predict_keep_raw": false,
"xorf_do_polishing": true,
"xorf_strip_truncations": true,
"xorf_skip_joined_concat": false,
"xorf_rename_deactivate": false,
"xorf_rename_rebase": true,
"xorf_rename_append_orf_score": true,
"xorf_rename_append_protein_name": true,
"xorf_rename_custom_prefix": null,
"xorf_samba_weights": "https://github.com/apcamargo/RNAsamba/raw/refs/heads/master/data/full_length_weights.hdf5",
"xorf_samba_local_weights": null,
"//6": "── Bigbed conversion [optional] ───────────────────────────────────────────",
"autosql": null,
"skip_bb_conversion": false
}