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Ensembl · Sep 3, 2024 · 3ad796f · 3ad796f
1 parent a39c8cf
commit 3ad796f
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Showing 2 changed files with 4 additions and 7 deletions.
diff --git a/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf b/pipelines/nextflow/modules/process_taxonomy_info/get_run_accessions.nf
@@ -41,14 +41,13 @@ process GET_RUN_ACCESSIONS {
     path("run_accession_list.txt")
 
     script:
-    //def runAccessionBatch = run_accession_batch ? run_accession_batch : null 
-     runAccessionList = []    
+    runAccessionList = []    
     runAccessionToFile='run_accession_list.txt' 
     def fileBatch=new File(run_accession_batch)
     if (fileBatch.exists()){
         fileBatch.eachLine { line ->
                 runAccessionList.add([taxon_id: taxon_id, gca: gca, run_accession: line])
-}   
+    }   
     """
     cat ${run_accession_batch.toString()} > $runAccessionToFile
     """
@@ -89,8 +88,6 @@ process GET_RUN_ACCESSIONS {
     }
     reader.close()
 
-//    runAccessionToFile='run_accession_list.txt'
-    //cp $run_accession_batch $runAccessionToFile
     log.info("BATCH FILE ${run_accession_batch}")
     """ 
     echo '${responseContent.toString()}' > $runAccessionToFile

diff --git a/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf b/pipelines/nextflow/modules/transcriptomic_alignment/index_genome.nf
@@ -70,8 +70,8 @@ process INDEX_GENOME {
     // Calculate the genome length (excluding header lines)
     //def genomeLength = fastaContent.split('\n').findAll { !it.startsWith('>') }.join('').length()
 
-     if (genomeLength != 0) {
-       filesValid = true
+    if (genomeLength != 0) {
+        filesValid = true
         }
     }
     // Define read length (you may need to adjust this based on your data)