Merge pull request #118 from theiagen/smw-basespace-fix-dev

BaseSpace_Fetch: convert periods to dashes
theiagen · Jul 18, 2023 · cb95c78 · cb95c78
2 parents 61c8d89 + 1ede00c
commit cb95c78
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/workflows/utilities/data_import/wf_basespace_fetch.wdl b/workflows/utilities/data_import/wf_basespace_fetch.wdl
@@ -99,7 +99,7 @@ task fetch_bs {
     # rename FASTQ files to add back in underscores that Illumina/Basespace changed into hyphens
     echo "Concatenating and renaming FASTQ files to add back underscores in basespace_sample_name"
     # setting a new bash variable to use for renaming during concatenation of FASTQs
-    SAMPLENAME_HYPHEN_INSTEAD_OF_UNDERSCORES=$(echo $sample_identifier | sed 's|_|-|g')
+    SAMPLENAME_HYPHEN_INSTEAD_OF_UNDERSCORES=$(echo $sample_identifier | sed 's|_|-|g' | sed 's|\.|-|g')
 
     #Combine non-empty read files into single file without BaseSpace filename cruft
     ##FWD Read