mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 05:49:56 +00:00
Remove --pep parameter and leave just --input
This commit is contained in:
parent
768f9980d8
commit
9349346864
12 changed files with 37 additions and 35 deletions
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@ -73,7 +73,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
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nextflow run nf-core/taxprofiler --input samplesheet.csv --databases database.csv --outdir <OUTDIR> --run_<TOOL1> --run_<TOOL1> -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
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```
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Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
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Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
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## Documentation
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@ -421,4 +421,12 @@ process {
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saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
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]
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}
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withName: 'EIDO_VALIDATE' {
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ext.args = '--st-index sample'
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}
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withName: 'EIDO_CONVERT' {
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ext.args = '--st-index sample'
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}
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}
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@ -8,8 +8,7 @@ params {
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max_time = '6.h'
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// Input data
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input = null
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pep = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
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input = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
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databases = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
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perform_shortread_qc = true
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perform_longread_qc = true
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@ -41,10 +40,4 @@ process {
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withName: MEGAN_RMA2INFO {
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maxForks = 1
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}
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withName: 'EIDO_VALIDATE' {
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ext.args = '--st-index sample'
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}
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withName: 'EIDO_CONVERT' {
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ext.args = '--st-index sample'
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}
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}
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@ -74,8 +74,8 @@ class WorkflowMain {
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NfcoreTemplate.awsBatch(workflow, params)
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// Check input has been provided
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if (!params.input && !params.pep) {
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log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
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if (!params.input) {
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log.error "Please provide an input samplesheet or PEP to the pipeline e.g. '--input samplesheet.csv'"
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System.exit(1)
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}
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}
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@ -43,11 +43,11 @@
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},
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"eido/convert": {
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"branch": "master",
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"git_sha": "c9b29c76869d9713130a13a418c1e8b5aecfb80d"
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"git_sha": "9764eef361ded86e9242075bda64c2662421386a"
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},
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"eido/validate": {
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"branch": "master",
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"git_sha": "8c0127e071711cb0a2648a6bdf881637a9d7eadc"
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"git_sha": "38383cfaefc06cd35e25de99989a3e6ab9ed2980"
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},
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"fastp": {
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"branch": "master",
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1
modules/nf-core/modules/eido/convert/main.nf
generated
1
modules/nf-core/modules/eido/convert/main.nf
generated
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@ -10,6 +10,7 @@ process EIDO_CONVERT {
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input:
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path samplesheet
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val format
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path pep_input_base_dir
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output:
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path "versions.yml" , emit: versions
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3
modules/nf-core/modules/eido/convert/meta.yml
generated
3
modules/nf-core/modules/eido/convert/meta.yml
generated
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@ -22,6 +22,9 @@ input:
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- format:
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type: value
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description: Extension of an output file
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- pep_input_base_dir:
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type: file
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description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
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output:
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- versions:
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1
modules/nf-core/modules/eido/validate/main.nf
generated
1
modules/nf-core/modules/eido/validate/main.nf
generated
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@ -10,6 +10,7 @@ process EIDO_VALIDATE {
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input:
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path samplesheet
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path schema
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path pep_input_base_dir
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output:
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path "versions.yml" , emit: versions
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3
modules/nf-core/modules/eido/validate/meta.yml
generated
3
modules/nf-core/modules/eido/validate/meta.yml
generated
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@ -23,6 +23,9 @@ input:
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type: file
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description: Schema that the samplesheet will be validated against
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pattern: "*.{yaml,yml}"
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- pep_input_base_dir:
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type: file
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description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory.
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output:
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- versions:
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@ -12,7 +12,6 @@ params {
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// TODO nf-core: Specify your pipeline's command line flags
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// Input options
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input = null
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pep = null
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// References
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@ -10,18 +10,13 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["outdir", "databases"],
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"required": ["outdir", "databases", "input"],
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"properties": {
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"pep": {
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"type": "string",
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"format": "file-path",
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"pattern": "^\\S+\\.yaml$"
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},
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"input": {
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"type": "string",
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"format": "file-path",
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"mimetype": "text/csv",
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"pattern": "^\\S+\\.csv$",
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"pattern": "^\\S+\\.(csv|yaml)$",
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"schema": "assets/schema_input.json",
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"description": "Path to comma-separated file containing information about the samples and libraries/runs.",
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"help_text": "You will need to create a design file with information about the samples and libraries/runs you want to running in your pipeline run. Use this parameter to specify its location. It has to be a comma-separated file with 6 columns, and a header row. See [usage docs](https://nf-co.re/taxprofiler/usage#samplesheet-input).",
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@ -17,23 +17,22 @@ def checkPathParamList = [ params.input, params.databases, params.hostremoval_re
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for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
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// Check mandatory parameters
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if (params.input) {
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if ( params.input.endsWith(".yaml") ) {
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if ( params.input.startsWith("http://") || params.input.startsWith("https://") ) {
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ch_input = file(params.input)
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ch_pep_input_base_dir = []
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}
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else {
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ch_input = file(params.input)
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ch_pep_input_base_dir = new File(params.input).getParent()
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}
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} else if ( params.input.endsWith(".csv") ) {
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ch_input = file(params.input)
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ch_pep_input_base_dir = []
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} else if (params.pep) {
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if ( params.pep.startsWith("http://") || params.pep.startsWith("https://") ) {
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ch_input = file(params.pep)
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ch_pep_input_base_dir = []
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}
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else {
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ch_input = file(params.pep)
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ch_pep_input_base_dir = new File(params.pep).getParent()
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}
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} else {
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} else {
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exit 1, 'Input samplesheet or PEP config not specified!'
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}
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