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feat: Add evolCCM entry #174

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Nov 5, 2023
Merged

feat: Add evolCCM entry #174

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92fea91
feat: Add evolCCM entry
jvfe Nov 3, 2023
359942b
refactor: Keep mandatory param check to workflows
jvfe Nov 4, 2023
f5a4e56
chore: Update schema
jvfe Nov 4, 2023
f70086a
refactor: Remove input_sample_table check from lib
jvfe Nov 4, 2023
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3 changes: 2 additions & 1 deletion docs/params.md
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Expand Up @@ -95,8 +95,9 @@ Parameters for the recombination subworkflow
| `min_branch_length` | Minimum rSPR branch length | `integer` | 0 | | |
| `max_support_threshold` | Maximum rSPR support threshold | `number` | 0.7 | | |
| `max_approx_rspr` | Maximum approximate rSPR distance for filtering | `integer` | -1 | | |
| `core_gene_tree` | Core (or reference) genome tree. Used in the rSPR entry. | `string` | | | |
| `core_gene_tree` | Core (or reference) genome tree. Used in the rSPR and evolCCM entries. | `string` | | | |
| `concatenated_annotation` | TSV table of annotations for all genomes. Such as the ones generated by Bakta or Prokka in ARETE. | `string` | | | |
| `feature_profile` | Feature profile TSV (A presence-absence matrix). Used in the evolCCM entry. | `string` | | | |

## Institutional config options

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5 changes: 0 additions & 5 deletions lib/WorkflowArete.groovy
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Expand Up @@ -66,11 +66,6 @@ class WorkflowArete {
// Check the hostnames against configured profiles
NfcoreTemplate.hostName(workflow, params, log)

// Check input has been provided
if (!params.input_sample_table) {
log.error "Please provide an input samplesheet to the pipeline e.g. '--input_sample_table samplesheet.csv'"
System.exit(1)
}
}

//
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5 changes: 5 additions & 0 deletions main.nf
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Expand Up @@ -38,6 +38,7 @@ include { PHYLO } from './workflows/arete'
include { QUALITYCHECK } from './workflows/arete'
include { POPPUNK } from './workflows/arete'
include { RUN_RSPR } from './workflows/arete'
include { RUN_EVOLCCM } from './workflows/arete'


//
Expand Down Expand Up @@ -72,6 +73,10 @@ workflow poppunk {
workflow rspr {
RUN_RSPR()
}

workflow evolccm {
RUN_EVOLCCM()
}
/*
========================================================================================
RUN ALL WORKFLOWS
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3 changes: 2 additions & 1 deletion nextflow.config
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Expand Up @@ -66,9 +66,10 @@ params {
max_support_threshold = 0.7
max_approx_rspr = -1

// rSPR entry
// rSPR/evolCCM entries
core_gene_tree = null
concatenated_annotation = null
feature_profile = null

// MultiQC options
multiqc_config = null
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10 changes: 7 additions & 3 deletions nextflow_schema.json
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Expand Up @@ -10,7 +10,7 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input_sample_table"],
"required": [],
"properties": {
"input_sample_table": {
"type": "string",
Expand Down Expand Up @@ -217,7 +217,7 @@
},
"accessory_similarity": {
"type": "number",
"default": 99,
"default": 99.0,
"fa_icon": "far fa-clone",
"description": "Similarity threshold for accessory genes"
}
Expand Down Expand Up @@ -282,11 +282,15 @@
},
"core_gene_tree": {
"type": "string",
"description": "Core (or reference) genome tree. Used in the rSPR entry."
"description": "Core (or reference) genome tree. Used in the rSPR and evolCCM entries."
},
"concatenated_annotation": {
"type": "string",
"description": "TSV table of annotations for all genomes. Such as the ones generated by Bakta or Prokka in ARETE."
},
"feature_profile": {
"type": "string",
"description": "Feature profile TSV (A presence-absence matrix). Used in the evolCCM entry."
}
},
"fa_icon": "fas fa-bezier-curve"
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14 changes: 10 additions & 4 deletions workflows/arete.nf
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Expand Up @@ -11,10 +11,6 @@ def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
def checkPathParamList = [ params.input_sample_table, params.multiqc_config, params.reference_genome ]
for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }

// Check mandatory parameters
if (params.input_sample_table) { ch_input = file(params.input_sample_table) } else { exit 1, 'Input samplesheet not specified!' }


/*
========================================================================================
CONFIG FILES
Expand Down Expand Up @@ -609,6 +605,16 @@ workflow RUN_RSPR {
)
}

workflow RUN_EVOLCCM {
if (params.core_gene_tree) { ch_core = file(params.core_gene_tree) } else { exit 1, 'Core tree not specified!' }
if (params.feature_profile) { ch_input = file(params.feature_profile) } else { exit 1, 'Input feature profile not specified!' }

EVOLCCM (
ch_core,
ch_input
)
}

/*
========================================================================================
COMPLETION EMAIL AND SUMMARY
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