validate input in main.nf

nf-core · Aug 25, 2023 · 1be5ebc · 1be5ebc
1 parent 6355a33
commit 1be5ebc
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Showing 3 changed files with 33 additions and 32 deletions.
diff --git a/main.nf b/main.nf
@@ -36,6 +36,36 @@ else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' }
 else                                         { exit 1, 'Ids provided via --input not recognised please make sure they are either SRA / ENA / GEO / DDBJ or Synapse ids!' }
 if (params.input_type != input_type)         { exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!" }
 
+/*
+========================================================================================
+    VALIDATE INPUTS
+========================================================================================
+*/
+
+if (params.input_type == 'sra') {
+    def valid_params = [
+        ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
+    ]
+
+    def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+    // Validate input parameters
+    WorkflowSra.initialise(params, valid_params)
+}
+
+if (params.input_type == 'synapse') {
+
+    def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+
+    // Create channel for synapse config
+    if (params.synapse_config) {
+        ch_synapse_config = file(params.synapse_config, checkIfExists: true)
+    } else {
+        exit 1, 'Please provide a Synapse config file for download authentication!'
+    }
+
+}
+
 /*
 ========================================================================================
     IMPORT MODULES
@@ -84,7 +114,7 @@ workflow NFCORE_FETCHNGS {
     // WORKFLOW: Download FastQ files for Synapse ids
     //
     } else if (params.input_type == 'synapse') {
-        SYNAPSE ( ch_ids )
+        SYNAPSE(ch_ids, ch_synapse_config)
         ch_versions = ch_versions.mix(SYNAPSE.out.versions)
     }
 

diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
@@ -1,18 +1,3 @@
-/*
-========================================================================================
-    VALIDATE INPUTS
-========================================================================================
-*/
-
-def valid_params = [
-    ena_metadata_fields : ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
-]
-
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
-
-// Validate input parameters
-WorkflowSra.initialise(params, valid_params)
-
 /*
 ========================================================================================
     IMPORT LOCAL MODULES/SUBWORKFLOWS

diff --git a/workflows/synapse/main.nf b/workflows/synapse/main.nf
@@ -1,18 +1,3 @@
-/*
-========================================================================================
-    VALIDATE INPUTS
-========================================================================================
-*/
-
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
-
-// Create channel for synapse config
-if (params.synapse_config) {
-    ch_synapse_config = file(params.synapse_config, checkIfExists: true)
-} else {
-    exit 1, 'Please provide a Synapse config file for download authentication!'
-}
-
 /*
 ========================================================================================
     IMPORT LOCAL MODULES/SUBWORKFLOWS
@@ -34,7 +19,8 @@ include { SYNAPSE_MERGE_SAMPLESHEET } from '../../modules/local/synapse_merge_sa
 workflow SYNAPSE {
 
     take:
-    ids // channel: [ ids ]
+    ids               // channel: [ ids ]
+    ch_synapse_config // channel: [ synapse_config ]
 
     main:
     ch_versions = Channel.empty()