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nf-core · May 16, 2024 · 5ef2f60 · 5ef2f60
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diff --git a/docs/usage.md b/docs/usage.md
@@ -511,7 +511,6 @@ nextflow run nf-core/airrflow -r dev \
 - The 10xGenomics reference can be downloaded from the [download page](https://www.10xgenomics.com/support/software/cell-ranger/downloads)
 - To generate a V(D)J segment fasta file as reference from IMGT one can follow the [cellranger docs](https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references#imgt).
 
-
 ## Supported unselected RNA-seq based methods
 
 nf-core/airrflow supports unselected bulk or single-cell RNA-seq fastq files as input. [TRUST4](https://github.com/liulab-dfci/TRUST4) is used to extract TCR/BCR sequences from these files. The resulting AIRR tables are then fed into airrflow's Immcantation based workflow. <br>
@@ -547,8 +546,8 @@ nextflow run nf-core/airrfow \
 --outdir results
 ```
 
-* If UMI's are present, the read containing them must be specified using the `--umi_position` parameter.
-* The `--read_format` parameter can be used to specify the Barcode and UMI position within the reads (see TRUST4 [docs](https://github.com/liulab-dfci/TRUST4?tab=readme-ov-file#10x-genomics-data-and-barcode-based-single-cell-data))
+- If UMI's are present, the read containing them must be specified using the `--umi_position` parameter.
+- The `--read_format` parameter can be used to specify the Barcode and UMI position within the reads (see TRUST4 [docs](https://github.com/liulab-dfci/TRUST4?tab=readme-ov-file#10x-genomics-data-and-barcode-based-single-cell-data))
 
 #### Reference file
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -130,7 +130,6 @@
             "properties": {
                 "umi_position": {
                     "type": "string",
-                    "default": "R1",
                     "description": "Indicate if UMI indices are recorded in the R1 (default) or R1 fastq file.",
                     "help_text": "The pipeline requires UMI barcodes for identifying unique transcripts. These barcodes are typically read from an index file but sometimes can be provided merged with the start of the R1 or R2 reads. If provided in an additional index file, set the `--index_file` parameter, if provided merged with the R1 or R2 reads, set the `--umi_position` parameter to R1 or R2, respectively.",
                     "enum": ["R1", "R2"],