Merge pull request #190 from maxulysse/better_syntax

tiny refactor
nf-core · Aug 25, 2023 · 493a544 · 493a544
2 parents 54e7d7d + 698fab1
commit 493a544
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Showing 3 changed files with 64 additions and 82 deletions.
diff --git a/main.nf b/main.nf
@@ -1,70 +1,94 @@
 #!/usr/bin/env nextflow
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     nf-core/fetchngs
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     Github : https://github.com/nf-core/fetchngs
     Website: https://nf-co.re/fetchngs
     Slack  : https://nfcore.slack.com/channels/fetchngs
-----------------------------------------------------------------------------------------
+========================================================================================
 */
 
 nextflow.enable.dsl = 2
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     VALIDATE & PRINT PARAMETER SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
 
 WorkflowMain.initialise(workflow, params, log)
 
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
-if (ch_input.isEmpty()) {exit 1, "File provided with --input is empty: ${ch_input.getName()}!"}
+if (ch_input.isEmpty()) { error("File provided with --input is empty: ${ch_input.getName()}!") }
 
 // Read in ids from --input file
-Channel
-    .from(file(params.input, checkIfExists: true))
+ch_ids = Channel.from(file(params.input, checkIfExists: true))
     .splitCsv(header:false, sep:'', strip:true)
     .map { it[0] }
     .unique()
-    .set { ch_ids }
+
+// Auto-detect input type
+def input_type = ''
+if (WorkflowMain.isSraId(ch_input))          { input_type = 'sra' }
+else if (WorkflowMain.isSynapseId(ch_input)) { input_type = 'synapse' }
+else                                         { error('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)         { error("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 {
+        error('Please provide a Synapse config file for download authentication!')
+    }
+
+}
 
 /*
 ========================================================================================
-    IMPORT MODULES/SUBWORKFLOWS
+    IMPORT MODULES
 ========================================================================================
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from './modules/nf-core/custom/dumpsoftwareversions'
 include { MULTIQC_MAPPINGS_CONFIG     } from './modules/local/multiqc_mappings_config'
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
+    IMPORT WORKFLOWS
+========================================================================================
 */
 
-// Auto-detect input id type
-def input_type = ''
-if (WorkflowMain.isSraId(ch_input)) {
-    input_type = 'sra'
-} 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 == 'sra')     include { SRA     } from './workflows/sra'
+if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
 
-if (params.input_type == input_type) {
-    if (params.input_type == 'sra') {
-        include { SRA } from './workflows/sra'
-    } else if (params.input_type == 'synapse') {
-        include { SYNAPSE } from './workflows/synapse'
-    }
-} else {
-    exit 1, "Ids auto-detected as ${input_type}. Please provide '--input_type ${input_type}' as a parameter to the pipeline!"
-}
+/*
+========================================================================================
+    NAMED WORKFLOW FOR PIPELINE
+========================================================================================
+*/
 
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
@@ -77,20 +101,20 @@ workflow NFCORE_FETCHNGS {
     // WORKFLOW: Download FastQ files for SRA / ENA / GEO / DDBJ ids
     //
     if (params.input_type == 'sra') {
-        SRA ( ch_ids )
+        SRA(ch_ids)
         ch_versions = ch_versions.mix(SRA.out.versions)
     //
     // MODULE: Create a MultiQC config file with sample name mappings
     //
         if (params.sample_mapping_fields) {
-            MULTIQC_MAPPINGS_CONFIG (SRA.out.mappings)
+            MULTIQC_MAPPINGS_CONFIG(SRA.out.mappings)
             ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         }
     //
     // 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)
     }
 
@@ -127,11 +151,12 @@ workflow.onComplete {
         NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
     }
     NfcoreTemplate.summary(workflow, params, log)
-    WorkflowSra.curateSamplesheetWarn(log)
+    if (params.input_type == 'sra')     { WorkflowSra.curateSamplesheetWarn(log) }
+    if (params.input_type == 'synapse') { WorkflowSynapse.curateSamplesheetWarn(log) }
 }
 
 /*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
     THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+========================================================================================
 */
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()
@@ -125,20 +111,6 @@ workflow SYNAPSE {
         versions    = ch_versions.unique()
 }
 
-/*
-========================================================================================
-    COMPLETION EMAIL AND SUMMARY
-========================================================================================
-*/
-
-workflow.onComplete {
-    if (params.email || params.email_on_fail) {
-        NfcoreTemplate.email(workflow, params, summary_params, projectDir, log)
-    }
-    NfcoreTemplate.summary(workflow, params, log)
-    WorkflowSynapse.curateSamplesheetWarn(log)
-}
-
 /*
 ========================================================================================
     THE END