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Merge pull request #10 from itrujnara/dev
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Updated modules.config
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@itrujnara
itrujnara committed Apr 29, 2024
2 parents e4f98ab + b77de4e commit 0f5159b
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Showing 7 changed files with 149 additions and 63 deletions.
156 changes: 132 additions & 24 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -18,26 +18,9 @@ process {
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]

withName: FASTQC {
ext.args = '--quiet'
}

withName: CUSTOM_DUMPSOFTWAREVERSIONS {
publishDir = [
path: { "${params.outdir}/pipeline_info" },
mode: params.publish_dir_mode,
pattern: '*_versions.yml'
]
}

withName: 'MULTIQC' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
path: { "${params.outdir}/multiqc" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}
// ----------------------
// Ortholog finding
// ----------------------

withName: 'IDENTIFY_SEQ_ONLINE|WRITE_SEQINFO' {
publishDir = [
Expand All @@ -63,14 +46,22 @@ process {
]
}

withName: 'FETCH_INSPECTOR_GROUP_ONLINE' {
withName: 'FETCH_INSPECTOR_GROUP_LOCAL|FETCH_INSPECTOR_GROUP_ONLINE' {
publishDir = [
path: { "${params.outdir}/orthologs/orthoinspector" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FETCH_EGGNOG_GROUP_LOCAL|FETCH_EGGNOG_GROUP_ONLINE' {
publishDir = [
path: { "${params.outdir}/orthologs/eggnog" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'MERGE_CSV' {
ext.args = '-f 1 --outer-join --na 0'
publishDir = [
Expand Down Expand Up @@ -104,13 +95,130 @@ process {
]
}

withName: 'MAKE_STATS' {
publishDir = [
path: { "${params.outdir}/orthologs/stats" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

// ----------------------
// Sequence alignment
// ----------------------

withName: 'FETCH_SEQUENCES_ONLINE' {
publishDir = [
path: { "${params.outdir}/sequences" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FETCH_AFDB_STRUCTURES' {
publishDir = [
path: { "${params.outdir}/structures" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FILTER_FASTA' {
publishDir = [
path: { "${params.outdir}/alignment/filter" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'CREATE_TCOFFEETEMPLATE' {
publishDir = [
path: { "${params.outdir}/alignment/template" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'TCOFFEE_ALIGN|TCOFFEE_3DALIGN' {
publishDir = [
path: { "${params.outdir}/alignment/tcoffee" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

// ----------------------
// Tree reconstruction
// ----------------------

withName: 'CONVERT_PHYLIP' {
publishDir = [
path: { "${params.outdir}/trees/convert" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'IQTREE' {
ext.args = '-m TEST' + (params.iqtree_bootstrap > 0 ? ' -bb ' + params.iqtree_bootstrap : '')
publishDir = [
path: { "${params.outdir}/trees/iqtree" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'PLOT_IQTREE' {
publishDir = [
path: { "${params.outdir}/trees/plots" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'FASTME' {
ext.args = '-p LG'
ext.args = '-p LG' + (params.fastme_bootstrap > 0 ? ' -b ' + params.fastme_bootstrap : '')
publishDir = [
path: { "${params.outdir}/trees/fastme" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'PLOT_ORTHOLOGS' {
ext.args = ''
withName: 'PLOT_FASTME' {
publishDir = [
path: { "${params.outdir}/trees/plots" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

// ----------------------
// Report generation
// ----------------------

withName: 'CONVERT_FASTA' {
publishDir = [
path: { "${params.outdir}/report/convert" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'DUMP_PARAMS' {
publishDir = [
path: { "${params.outdir}/report/params" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: 'MAKE_REPORT' {
publishDir = [
path: { "${params.outdir}/report" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

}
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2 changes: 1 addition & 1 deletion docs/images/reportho_tube_map.svg
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9 changes: 2 additions & 7 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -37,13 +37,8 @@ params {
use_structures = false
use_iqtree = true
use_fastme = false

// References
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
iqtree_bootstrap = 100
fastme_bootstrap = 100

// Boilerplate options
outdir = null
Expand Down
45 changes: 14 additions & 31 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,6 @@
"fa_icon": "fas fa-envelope",
"help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.",
"pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$"
},
"multiqc_title": {
"type": "string",
"description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.",
"fa_icon": "fas fa-file-signature"
}
}
},
Expand Down Expand Up @@ -216,6 +211,20 @@
"description": "Use FastME for the phylogenetic analysis.",
"help_text": "If set to `true`, the pipeline will use FastME for the phylogenetic analysis.",
"fa_icon": "fas fa-tree"
},
"iqtree_bootstrap": {
"type": "integer",
"default": 100,
"description": "Number of bootstrap replicates for IQ-TREE.",
"help_text": "If set to `0`, bootstrap will not be performed.",
"fa_icon": "fas fa-rotate"
},
"fastme_bootstrap": {
"type": "integer",
"default": 100,
"description": "Number of bootstrap replicates for FastME.",
"help_text": "If set to `0`, bootstrap will not be performed.",
"fa_icon": "fas fa-rotate"
}
}
},
Expand Down Expand Up @@ -344,14 +353,6 @@
"fa_icon": "fas fa-remove-format",
"hidden": true
},
"max_multiqc_email_size": {
"type": "string",
"description": "File size limit when attaching MultiQC reports to summary emails.",
"pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$",
"default": "25.MB",
"fa_icon": "fas fa-file-upload",
"hidden": true
},
"monochrome_logs": {
"type": "boolean",
"description": "Do not use coloured log outputs.",
Expand All @@ -365,24 +366,6 @@
"help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.",
"hidden": true
},
"multiqc_config": {
"type": "string",
"format": "file-path",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
},
"multiqc_logo": {
"type": "string",
"description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
"fa_icon": "fas fa-image",
"hidden": true
},
"multiqc_methods_description": {
"type": "string",
"description": "Custom MultiQC yaml file containing HTML including a methods description.",
"fa_icon": "fas fa-cog"
},
"validate_params": {
"type": "boolean",
"description": "Boolean whether to validate parameters against the schema at runtime",
Expand Down

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