Remove --pep parameter and leave just --input

README.md

@@ -73,7 +73,7 @@ On release, automated continuous integration tests run the pipeline on a full-si
    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>
    ```
 
-  Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
+Note pipeline supports both CSV and PEP input sample sheets. Find out more [here](http://pep.databio.org/en/2.1.0/specification/).
 
 ## Documentation
 

conf/modules.config

@@ -421,4 +421,12 @@ process {
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
     }
+
+    withName: 'EIDO_VALIDATE' {
+        ext.args = '--st-index sample'
+    }
+
+    withName: 'EIDO_CONVERT' {
+        ext.args = '--st-index sample'
+    }
 }

conf/test_pep.config

@@ -8,8 +8,7 @@ params {
     max_time   = '6.h'
 
     // Input data
-    input                                 = null
-    pep                                   = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
+    input                                 = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/pep/test_pep_format_files/config.yaml'
     databases                             = 'https://raw.githubusercontent.com/nf-core/test-datasets/taxprofiler/database.csv'
     perform_shortread_qc                  = true
     perform_longread_qc                   = true
@@ -41,10 +40,4 @@ process {
     withName: MEGAN_RMA2INFO {
         maxForks = 1
     }
-    withName: 'EIDO_VALIDATE' {
-        ext.args = '--st-index sample'
-    }
-    withName: 'EIDO_CONVERT' {
-        ext.args = '--st-index sample'
-    }
 }

lib/WorkflowMain.groovy

@@ -74,8 +74,8 @@ class WorkflowMain {
         NfcoreTemplate.awsBatch(workflow, params)
 
         // Check input has been provided
-        if (!params.input && !params.pep) {
-            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
+        if (!params.input) {
+            log.error "Please provide an input samplesheet or PEP to the pipeline e.g. '--input samplesheet.csv'"
             System.exit(1)
         }
     }

modules.json

@@ -43,11 +43,11 @@
                 },
                 "eido/convert": {
                     "branch": "master",
-                    "git_sha": "c9b29c76869d9713130a13a418c1e8b5aecfb80d"
+                    "git_sha": "9764eef361ded86e9242075bda64c2662421386a"
                 },
                 "eido/validate": {
                     "branch": "master",
-                    "git_sha": "8c0127e071711cb0a2648a6bdf881637a9d7eadc"
+                    "git_sha": "38383cfaefc06cd35e25de99989a3e6ab9ed2980"
                 },
                 "fastp": {
                     "branch": "master",

modules/nf-core/modules/eido/convert/main.nf

@@ -10,6 +10,7 @@ process EIDO_CONVERT {
     input:
     path samplesheet
     val format
+    path pep_input_base_dir
 
     output:
     path "versions.yml"           , emit: versions

modules/nf-core/modules/eido/convert/meta.yml

@@ -22,6 +22,9 @@ input:
   - format:
       type: value
       description: Extension of an output file
+  - pep_input_base_dir:
+      type: file
+      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.
 
 output:
   - versions:

modules/nf-core/modules/eido/validate/main.nf

@@ -10,6 +10,7 @@ process EIDO_VALIDATE {
     input:
     path samplesheet
     path schema
+    path pep_input_base_dir
 
     output:
     path "versions.yml"  , emit: versions

modules/nf-core/modules/eido/validate/meta.yml

@@ -23,6 +23,9 @@ input:
       type: file
       description: Schema that the samplesheet will be validated against
       pattern: "*.{yaml,yml}"
+  - pep_input_base_dir:
+      type: file
+      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.
 
 output:
   - versions:

nextflow.config

@@ -12,7 +12,6 @@ params {
     // TODO nf-core: Specify your pipeline's command line flags
     // Input options
     input                      = null
-    pep                        = null
 
 
     // References

nextflow_schema.json

@@ -10,18 +10,13 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["outdir", "databases"],
+            "required": ["outdir", "databases", "input"],
             "properties": {
-                "pep": {
-                    "type": "string",
-                    "format": "file-path",
-                    "pattern": "^\\S+\\.yaml$"
-                },
                 "input": {
                     "type": "string",
                     "format": "file-path",
                     "mimetype": "text/csv",
-                    "pattern": "^\\S+\\.csv$",
+                    "pattern": "^\\S+\\.(csv|yaml)$",
                     "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the samples and libraries/runs.",
                     "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).",

workflows/taxprofiler.nf

@@ -17,23 +17,22 @@ def checkPathParamList = [ params.input, params.databases, params.hostremoval_re
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
-if (params.input) {
+if ( params.input.endsWith(".yaml") ) {
+
+    if ( params.input.startsWith("http://") || params.input.startsWith("https://") ) {
+        ch_input = file(params.input)
+        ch_pep_input_base_dir = []
+    }
+    else {
+        ch_input = file(params.input)
+        ch_pep_input_base_dir = new File(params.input).getParent()
+    }
+
+} else if ( params.input.endsWith(".csv") ) {
     ch_input = file(params.input)
     ch_pep_input_base_dir = []
 
-} else if (params.pep) {
-
-    if ( params.pep.startsWith("http://") || params.pep.startsWith("https://") ) {
-        ch_input = file(params.pep)
-        ch_pep_input_base_dir = []
-    }
-
-    else {
-        ch_input = file(params.pep)
-        ch_pep_input_base_dir = new File(params.pep).getParent()
-    }
-
-}  else {
+} else {
     exit 1, 'Input samplesheet or PEP config not specified!'
 }