Merge pull request #238 from alexblaessle/sra_merge_samplesheet_large…

…_studies Resolved bug when prefetching large studies
nf-core · Jan 4, 2024 · f794ea3 · f794ea3
2 parents a6f7d52 + 87c94c0
commit f794ea3
Show file tree

Hide file tree

Showing 7 changed files with 7 additions and 117 deletions.
diff --git a/modules/local/sra_merge_samplesheet/main.nf b/modules/local/sra_merge_samplesheet/main.nf
diff --git a/modules/local/sra_merge_samplesheet/nextflow.config b/modules/local/sra_merge_samplesheet/nextflow.config
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test b/modules/local/sra_merge_samplesheet/tests/main.nf.test
diff --git a/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap b/modules/local/sra_merge_samplesheet/tests/main.nf.test.snap
diff --git a/modules/local/sra_merge_samplesheet/tests/tags.yml b/modules/local/sra_merge_samplesheet/tests/tags.yml
diff --git a/workflows/sra/main.nf b/workflows/sra/main.nf
@@ -7,7 +7,6 @@
 include { MULTIQC_MAPPINGS_CONFIG } from '../../modules/local/multiqc_mappings_config'
 include { SRA_FASTQ_FTP           } from '../../modules/local/sra_fastq_ftp'
 include { SRA_IDS_TO_RUNINFO      } from '../../modules/local/sra_ids_to_runinfo'
-include { SRA_MERGE_SAMPLESHEET   } from '../../modules/local/sra_merge_samplesheet'
 include { SRA_RUNINFO_TO_FTP      } from '../../modules/local/sra_runinfo_to_ftp'
 include { SRA_TO_SAMPLESHEET      } from '../../modules/local/sra_to_samplesheet'
 
@@ -118,32 +117,28 @@ workflow SRA {
         params.nf_core_rnaseq_strandedness ?: 'auto',
         params.sample_mapping_fields
     )
+
 
-    //
-    // MODULE: Create a merged samplesheet across all samples for the pipeline
-    //
-    SRA_MERGE_SAMPLESHEET (
-        SRA_TO_SAMPLESHEET.out.samplesheet.collect{it[1]},
-        SRA_TO_SAMPLESHEET.out.mappings.collect{it[1]}
-    )
-    ch_versions = ch_versions.mix(SRA_MERGE_SAMPLESHEET.out.versions)
+    // Combine all sample sheet/mapping paths into two files
+    ch_samplesheet=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'samplesheets.csv', newLine: true, keepHeader: true, storeDir:params.outdir)
+    ch_mappings=SRA_TO_SAMPLESHEET.out.samplesheet.map{it[1]}.collectFile(name:'id_mappings.csv', newLine: true, keepHeader: true, storeDir:params.outdir)
 
     //
     // MODULE: Create a MutiQC config file with sample name mappings
     //
     ch_sample_mappings_yml = Channel.empty()
     if (params.sample_mapping_fields) {
         MULTIQC_MAPPINGS_CONFIG (
-            SRA_MERGE_SAMPLESHEET.out.mappings
+            ch_mappings
         )
         ch_versions = ch_versions.mix(MULTIQC_MAPPINGS_CONFIG.out.versions)
         ch_sample_mappings_yml = MULTIQC_MAPPINGS_CONFIG.out.yml
     }
 
     emit:
     fastq           = fastq_files
-    samplesheet     = SRA_MERGE_SAMPLESHEET.out.samplesheet
-    mappings        = SRA_MERGE_SAMPLESHEET.out.mappings
+    samplesheet     = ch_samplesheet
+    mappings        = ch_mappings
     sample_mappings = ch_sample_mappings_yml
     versions        = ch_versions.unique()
 }

diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config
@@ -1,7 +1,6 @@
 includeConfig "../../modules/local/multiqc_mappings_config/nextflow.config"
 includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config"
-includeConfig "../../modules/local/sra_merge_samplesheet/nextflow.config"
 includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config"
 includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config"
 includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config"