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Multiple modifications calling #46

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Multiple modifications calling #46

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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -124,7 +124,7 @@ The folder may contain other folders of FAST5 or POD5 files and all files will b
|--------------------------|------|-------------|------|---------|
| basecaller_cfg | string | Name of the model to use for converting signal. | Required for basecalling. The model list only shows models that are compatible with this workflow. | |
| duplex | boolean | Run the basecaller in duplex mode. | By default the workflow conducts simplex basecalling. If you used a chemistry and flowcell combination that supports duplex reads, you may switch this option on. This option is incompatible with the watch_path option due to the way the input files must be traversed in order to find duplex pairs. | False |
| remora_cfg | string | Name of the model to use for calling modified bases. | Required for calling modified bases while basecalling. The model list only shows models that are compatible with this workflow. | |
| remora_cfg | string<br>(array) | Name of the model to use for calling modified bases. | Required for calling modified bases while basecalling. The model list only shows models that are compatible with this workflow. Provide multiple models as an array of names via the `-params-file` argument. | |
| dorado_ext | string | File extension for Dorado inputs. | Set this to fast5 if you have not converted your fast5 to pod5. It is recommended to [convert existing fast5 files to pod5 for use with Dorado](https://github.com/nanoporetech/pod5-file-format/blob/master/python/README.md#pod5-convert-from-fast5). | pod5 |
| poly_a_config | string | Provide this TOML file to turn on and configure dorado poly(A) calling. | This TOML file allows you to turn on and configure poly(A) tail calling options in dorado. This feature is described [here](https://github.com/nanoporetech/dorado?tab=readme-ov-file#polya-tail-estimation). | |
| barcode_kit | string | Name of the kit to use for barcoding. Demultiplex the data. | Providing a kit here will instruct the workflow to demultiplex your 'pass' data to BAM files which can be found in your output dir under the folder 'demuxed' in a struture reminissent of MinKNOW. | |
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2 changes: 1 addition & 1 deletion lib/signal/ingress.nf
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Expand Up @@ -51,7 +51,7 @@ process dorado {
path("${chunk_idx}.ubam"), emit: ubams
path("converted/*.pod5"), emit: converted_pod5s, optional: true
script:
def remora_model = remora_model_override ? "remora_model" : "\${DRD_MODELS_PATH}/${remora_cfg}"
def remora_model = remora_cfg instanceof String ? "\${DRD_MODELS_PATH}/${remora_cfg}" : remora_cfg.collect { "\${DRD_MODELS_PATH}/$it" }.join(',')
def remora_args = (params.basecaller_basemod_threads > 0 && (params.remora_cfg || remora_model_override)) ? "--modified-bases-models ${remora_model}" : ''
def model_arg = basecaller_model_override ? "dorado_model" : "\${DRD_MODELS_PATH}/${basecaller_cfg}"
def basecaller_args = params.basecaller_args ?: ''
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115 changes: 80 additions & 35 deletions nextflow_schema.json
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Expand Up @@ -118,42 +118,87 @@
},
"remora_cfg": {
"title": "Modified basecalling model configuration",
"type": "string",
"description": "Name of the model to use for calling modified bases.",
"help_text": "Required for calling modified bases while basecalling. The model list only shows models that are compatible with this workflow.",
"enum": [
"dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1",
"dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1",
"dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0",
"dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1",
"dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0",
"dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1",
"dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0",
"rna004_130bps_hac@v5.0.0_m6A@v1",
"rna004_130bps_hac@v5.0.0_pseU@v1",
"rna004_130bps_sup@v3.0.1_m6A_DRACH@v1",
"rna004_130bps_sup@v5.0.0_m6A@v1",
"rna004_130bps_sup@v5.0.0_pseU@v1"
"help_text": "Required for calling modified bases while basecalling. The model list only shows models that are compatible with this workflow. Provide multiple models as an array of names via the -params-file argument.",
"oneOf": [
{
"type": "array",
"items": {
"type": "string",
"enum": [
"dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1",
"dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1",
"dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0",
"dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1",
"dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0",
"dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1",
"dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0",
"rna004_130bps_hac@v5.0.0_m6A@v1",
"rna004_130bps_hac@v5.0.0_pseU@v1",
"rna004_130bps_sup@v3.0.1_m6A_DRACH@v1",
"rna004_130bps_sup@v5.0.0_m6A@v1",
"rna004_130bps_sup@v5.0.0_pseU@v1"
]
},
"uniqueItems": true
},
{
"type": "string",
"enum": [
"dna_r10.4.1_e8.2_260bps_fast@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_260bps_hac@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_260bps_sup@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_fast@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_fast@v4.2.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_hac@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v4.3.0_6mA@v2",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_4mC_5mC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_hac@v5.0.0_6mA@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.1.0_5mCG_5hmCG@v2",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v4.3.0_6mA@v2",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_4mC_5mC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mCG_5hmCG@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_5mC_5hmC@v1",
"dna_r10.4.1_e8.2_400bps_sup@v5.0.0_6mA@v1",
"dna_r9.4.1_e8_fast@v3.4_5mCG@v0.1",
"dna_r9.4.1_e8_fast@v3.4_5mCG_5hmCG@v0",
"dna_r9.4.1_e8_hac@v3.3_5mCG@v0.1",
"dna_r9.4.1_e8_hac@v3.3_5mCG_5hmCG@v0",
"dna_r9.4.1_e8_sup@v3.3_5mCG@v0.1",
"dna_r9.4.1_e8_sup@v3.3_5mCG_5hmCG@v0",
"rna004_130bps_hac@v5.0.0_m6A@v1",
"rna004_130bps_hac@v5.0.0_pseU@v1",
"rna004_130bps_sup@v3.0.1_m6A_DRACH@v1",
"rna004_130bps_sup@v5.0.0_m6A@v1",
"rna004_130bps_sup@v5.0.0_pseU@v1"
]
}
]
},
"dorado_ext": {
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