Merge pull request #125 from drpatelh/fixes

Fix #119
nf-core · Nov 7, 2022 · c08f84b · c08f84b
2 parents 44901cf + c791a37
commit c08f84b
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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.json b/modules.json
@@ -15,13 +15,21 @@
                     },
                     "sratools/fasterqdump": {
                         "branch": "master",
-                        "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
+                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2"
                     },
                     "sratools/prefetch": {
                         "branch": "master",
                         "git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
                     }
                 }
+            },
+            "subworkflows": {
+                "nf-core": {
+                    "fastq_download_prefetch_fasterqdump_sratools": {
+                        "branch": "master",
+                        "git_sha": "03711bcb7fa2a7088eb54abb1fca326d30e602c2"
+                    }
+                }
             }
         }
     }

diff --git a/modules/nf-core/sratools/fasterqdump/main.nf b/modules/nf-core/sratools/fasterqdump/main.nf
diff --git a/nextflow.config b/nextflow.config
@@ -174,7 +174,7 @@ manifest {
     description     = 'Pipeline to fetch metadata and raw FastQ files from public databases'
     mainScript      = 'main.nf'
     nextflowVersion = '!>=21.10.3'
-    version         = '1.8dev'
+    version         = '1.8'
     doi             = 'https://doi.org/10.5281/zenodo.5070524'
 }
 

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