Merge pull request #209 from drpatelh/fixes

Minor pre-release tweaks and bug fixes

Author: drpatelh

CHANGELOG.md

@@ -12,15 +12,29 @@ Special thanks to the following for their contributions to the release:
 - [Adam Talbot](https://github.com/adamrtalbot)
 - [Harshil Patel](https://github.com/drpatelh)
 - [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
 
 Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 
+- [#173](https://github.com/nf-core/fetchngs/issues/173) - Add compatibility for sralite files
 - [PR #205](https://github.com/nf-core/fetchngs/pull/205) - Rename all local modules, workflows and remove `public_aws_ecr profile`
 - [PR #206](https://github.com/nf-core/fetchngs/pull/206) - CI improvments and code cleanup
 - [PR #208](https://github.com/nf-core/fetchngs/pull/208) - Template update with nf-core/tools 2.10
 
+### Software dependencies
+
+| Dependency  | Old version | New version |
+| ----------- | ----------- | ----------- |
+| `sra-tools` | 2.11.0      | 3.0.8       |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16
 
 ### Credits

lib/WorkflowSra.groovy

@@ -9,11 +9,12 @@ class WorkflowSra {
     //
     // Check and validate parameters
     //
-    public static void initialise(params, valid_params) {
+    public static void initialise(params) {
         // Check minimal ENA fields are provided to download FastQ files
-        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_params['ena_metadata_fields']
-        if (!ena_metadata_fields.containsAll(valid_params['ena_metadata_fields'])) {
-            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_params['ena_metadata_fields'].join(',')}'")
+        def valid_ena_metadata_fields = ['run_accession', 'experiment_accession', 'library_layout', 'fastq_ftp', 'fastq_md5']
+        def ena_metadata_fields = params.ena_metadata_fields ? params.ena_metadata_fields.split(',').collect{ it.trim().toLowerCase() } : valid_ena_metadata_fields
+        if (!ena_metadata_fields.containsAll(valid_ena_metadata_fields)) {
+            Nextflow.error("Invalid option: '${params.ena_metadata_fields}'. Minimally required fields for '--ena_metadata_fields': '${valid_ena_metadata_fields.join(',')}'")
         }
     }
 

main.nf

@@ -19,35 +19,25 @@ nextflow.enable.dsl = 2
 
 include { paramsHelp; paramsSummaryLog; validateParameters } from 'plugin/nf-validation'
 
+// Print parameter summary log to screen
 def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
 def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
-
-// Print help message if needed
+def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
 if (params.help) {
-    def String command = "nextflow run ${workflow.manifest.name} --input id.csv -profile docker"
     log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
     System.exit(0)
-}
-
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
+} else {
+    log.info logo + paramsSummaryLog(workflow) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
 }
 
 // Check if --input file is empty
 ch_input = file(params.input, checkIfExists: true)
 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))
-    .splitCsv(header:false, sep:'', strip:true)
-    .map { it[0] }
-    .unique()
-    .set { ch_ids }
+// Validate input parameters
+if (params.validate_params) {
+    validateParameters()
+}
 
 // Auto-detect input id type
 def input_type = ''
@@ -58,10 +48,19 @@ if (WorkflowMain.isSraId(ch_input)) {
 } 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!")
 }
 
+// Read in ids from --input file
+Channel
+    .from(file(params.input, checkIfExists: true))
+    .splitCsv(header:false, sep:'', strip:true)
+    .map { it[0] }
+    .unique()
+    .set { ch_ids }
+
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     IMPORT WORKFLOWS
@@ -71,6 +70,12 @@ if (params.input_type != input_type) {
 if (params.input_type == 'sra')     include { SRA     } from './workflows/sra'
 if (params.input_type == 'synapse') include { SYNAPSE } from './workflows/synapse'
 
+/*
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+    NAMED WORKFLOWS FOR PIPELINE
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+*/
+
 //
 // WORKFLOW: Run main nf-core/fetchngs analysis pipeline depending on type of identifier provided
 //

modules.json

@@ -17,12 +17,12 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
+                        "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
                         "branch": "master",
-                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
+                        "git_sha": "4d9951c6c9c4c19ea944bb73149caf9d3cb1f2fc",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     }
                 }
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "6712754854ae2832abfff3f0800cdb4a6a60bfca",
+                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
                         "installed_by": ["subworkflows"]
                     }
                 }

modules/nf-core/sratools/fasterqdump/main.nf

@@ -4,14 +4,11 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-include { paramsSummaryLog; paramsSummaryMap } from 'plugin/nf-validation'
+include { paramsSummaryMap } from 'plugin/nf-validation'
 
-def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
 def summary_params = paramsSummaryMap(workflow)
 
-// Print parameter summary log to screen
-log.info logo + paramsSummaryLog(workflow) + citation
+WorkflowSra.initialise(params)
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -33,7 +30,6 @@ include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_c
 */
 
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../../modules/nf-core/custom/dumpsoftwareversions/main'
-
 include { FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS } from '../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/main'
 
 /*

modules/nf-core/sratools/prefetch/main.nf

@@ -4,7 +4,9 @@
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params)
+include { paramsSummaryMap } from 'plugin/nf-validation'
+
+def summary_params = paramsSummaryMap(workflow)
 
 // Create channel for synapse config
 if (params.synapse_config) {