Fix nf-core#119

drpatelh · Nov 7, 2022 · 3172622 · 3172622
1 parent 44901cf
commit 3172622
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,13 +3,14 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-07
+## [[1.8](https://github.com/nf-core/fetchngs/releases/tag/1.8)] - 2022-11-08
 
 ### Enhancements & fixes
 
 - [#111](https://github.com/nf-core/fetchngs/issues/111) - Change input mimetype to csv
 - [#114](https://github.com/nf-core/fetchngs/issues/114) - Final samplesheet is not created when `--skip_fastq_download` is provided
 - [#118](https://github.com/nf-core/fetchngs/issues/118) - Allow input pattern validation for csv/tsv/txt
+- [#119](https://github.com/nf-core/fetchngs/issues/119) - `--force_sratools_download` results in different fastq names compared to FTP download 
 - [#121](https://github.com/nf-core/fetchngs/issues/121) - Add `tower.yml` to render samplesheet as Report in Tower
 - Fetch `SRR` and `DRR` metadata from ENA API instead of NCBI API to bypass frequent breaking changes
 - Updated pipeline template to [nf-core/tools 2.6](https://github.com/nf-core/tools/releases/tag/2.6)

diff --git a/conf/modules.config b/conf/modules.config
@@ -78,16 +78,9 @@ if (params.input_type == 'sra') {
 
         withName: SRATOOLS_FASTERQDUMP {
             publishDir = [
-                [
-                    path: { "${params.outdir}/fastq" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.fastq.gz"
-                ],
-                [
-                    path: { "${params.outdir}/fastq/md5" },
-                    mode: params.publish_dir_mode,
-                    pattern: "*.md5"
-                ]
+                path: { "${params.outdir}/fastq" },
+                mode: params.publish_dir_mode,
+                pattern: "*.fastq.gz"
             ]
         }
 

diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
diff --git a/subworkflows/nf-core/srafastq/main.nf → ...oad_prefetch_fasterqdump_sratools/main.nf b/subworkflows/nf-core/srafastq/main.nf → ...oad_prefetch_fasterqdump_sratools/main.nf
diff --git a/subworkflows/nf-core/srafastq/meta.yml → ...ad_prefetch_fasterqdump_sratools/meta.yml b/subworkflows/nf-core/srafastq/meta.yml → ...ad_prefetch_fasterqdump_sratools/meta.yml
diff --git a/workflows/sra.nf b/workflows/sra.nf
@@ -26,8 +26,6 @@ include { SRA_TO_SAMPLESHEET      } from '../modules/local/sra_to_samplesheet'
 include { SRA_MERGE_SAMPLESHEET   } from '../modules/local/sra_merge_samplesheet'
 include { MULTIQC_MAPPINGS_CONFIG } from '../modules/local/multiqc_mappings_config'
 
-include { SRAFASTQ                } from '../subworkflows/nf-core/srafastq/main'
-
 /*
 ========================================================================================
     IMPORT NF-CORE MODULES/SUBWORKFLOWS
@@ -36,6 +34,8 @@ include { SRAFASTQ                } from '../subworkflows/nf-core/srafastq/main'
 
 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'
+
 /*
 ========================================================================================
     RUN MAIN WORKFLOW
@@ -112,15 +112,15 @@ workflow SRA {
         //
         // SUBWORKFLOW: Download sequencing reads without FTP links using sra-tools.
         //
-        SRAFASTQ (
+        FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS (
             ch_sra_reads.sra.map { meta, reads -> [ meta, meta.run_accession ] }
         )
-        ch_versions = ch_versions.mix(SRAFASTQ.out.versions.first())
+        ch_versions = ch_versions.mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.versions.first())
 
         SRA_FASTQ_FTP
             .out
             .fastq
-            .mix(SRAFASTQ.out.reads)
+            .mix(FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS.out.reads)
             .map { 
                 meta, fastq ->
                     def reads = meta.single_end ? [ fastq ] : fastq