Add support to download 10X Genomics data

CHANGELOG.md

@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unpublished Version / DEV]
 
+- [#144](https://github.com/nf-core/fetchngs/issues/144) - Add support to download 10X Genomics data
 - Bumped modules version to allow for sratools download of sralite format files.
 
 ### Enhancements & fixes

conf/modules.config

@@ -77,6 +77,7 @@ if (params.input_type == 'sra') {
         }
 
         withName: SRATOOLS_FASTERQDUMP {
+            ext.args = '--split-files --include-technical'
             publishDir = [
                 path: { "${params.outdir}/fastq" },
                 mode: params.publish_dir_mode,

conf/test_full.config

@@ -15,5 +15,5 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test.csv'
+    input  = 'https://raw.githubusercontent.com/nf-core/test-datasets/fetchngs/sra_ids_test_full.csv'
 }

modules.json

@@ -17,7 +17,7 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "10cb20f6a130d104fef335a8290f3ffce650f28d",
                         "installed_by": ["fastq_download_prefetch_fasterqdump_sratools"]
                     },
                     "sratools/prefetch": {
@@ -31,7 +31,7 @@
                 "nf-core": {
                     "fastq_download_prefetch_fasterqdump_sratools": {
                         "branch": "master",
-                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2",
+                        "git_sha": "ca2bf9212707e83717934ec6c5d4cab42b39ca69",
                         "installed_by": ["subworkflows"]
                     }
                 }

workflows/sra.nf

@@ -123,7 +123,7 @@ workflow SRA {
             .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
             .map { 
                 meta, fastq ->
-                    def reads = meta.single_end ? [ fastq ] : fastq
+                    def reads = fastq instanceof List ? fastq.flatten() : [ fastq ]
                     def meta_clone = meta.clone()
                     meta_clone.fastq_1 = reads[0] ? "${params.outdir}/fastq/${reads[0].getName()}" : ''
                     meta_clone.fastq_2 = reads[1] && !meta.single_end ? "${params.outdir}/fastq/${reads[1].getName()}" : ''