Merge pull request #807 from MatthiasZepper/issue797-skip_umitools_extract

Issue797 skip umitools extract

Author: drpatelh

CHANGELOG.md

@@ -14,13 +14,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - [[#764](https://github.com/nf-core/rnaseq/issues/764)] - Test fails when using GCP due to missing tools in the basic biocontainer
 - [[#791](https://github.com/nf-core/rnaseq/issues/791)] - Add outputs for umitools dedup summary stats
+- [[#797](https://github.com/nf-core/rnaseq/issues/797)] - Add `--skip_umi_extract` to account for pre-existing UMIs header embeddings.
 - [[#798](https://github.com/nf-core/rnaseq/issues/798)] - Decompress transcript fasta error
 - [[#799](https://github.com/nf-core/rnaseq/issues/799)] - Issue with using `--retain_unpaired` with the `FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE` module
 - [[#802](https://github.com/nf-core/rnaseq/issues/802)] - `--bam_csi_index` error generated if `--skip_alignment` specified
 - [[#808](https://github.com/nf-core/rnaseq/issues/808)] - Auto-detect usage of Illumina iGenomes reference
 - [[#814](https://github.com/nf-core/rnaseq/issues/814)] - Use decimal values for `--min_mapped_reads`
 - Updated pipeline template to [nf-core/tools 2.3.2](https://github.com/nf-core/tools/releases/tag/2.3.2)
 
+### Parameters
+
+| Old parameter                 | New parameter                         |
+|-------------------------------|---------------------------------------|
+|                               | `--skip_umi_extract`                  |
+
 ### Software dependencies
 
 Note, since the pipeline is now using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

conf/modules.config

@@ -207,7 +207,7 @@ if (!params.skip_trimming) {
     }
 }
 
-if (params.with_umi) {
+if (params.with_umi && !params.skip_umi_extract) {
     process {
         withName: '.*:FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT' {
             ext.args   = [

docs/output.md

@@ -94,6 +94,8 @@ If multiple libraries/runs have been provided for the same sample in the input s
 
 [UMI-tools](https://github.com/CGATOxford/UMI-tools) deduplicates reads based on unique molecular identifiers (UMIs) to address PCR-bias. Firstly, the UMI-tools `extract` command removes the UMI barcode information from the read sequence and adds it to the read name. Secondly, reads are deduplicated based on UMI identifier after mapping as highlighted in the [UMI-tools dedup](#umi-tools-dedup) section.
 
+To facilitate processing of input data which has the UMI barcode already embedded in the read name from the start, `--skip_umi_extract` can be specified in conjunction with `--with_umi`.
+
 ### TrimGalore
 
 <details markdown="1">

nextflow.config

@@ -26,6 +26,7 @@ params {
 
     // UMI handling
     with_umi                   = false
+    skip_umi_extract           = false
     umitools_extract_method    = 'string'
     umitools_bc_pattern        = null
     umi_discard_read           = null

nextflow_schema.json

@@ -65,6 +65,11 @@
                     "description": "UMI pattern to use. Can be either 'string' (default) or 'regex'.",
                     "help_text": "More details can be found in the [UMI-tools documentation](https://umi-tools.readthedocs.io/en/latest/reference/extract.html#extract-method).\n"
                 },
+                "skip_umi_extract": {
+                    "type": "boolean",
+                    "fa_icon": "fas fa-compress-alt",
+                    "description": "Skip the UMI extraction from the read in case the UMIs have been moved to the headers in advance of the pipeline run."
+                },
                 "umitools_bc_pattern": {
                     "type": "string",
                     "fa_icon": "fas fa-barcode",

subworkflows/nf-core/fastqc_umitools_trimgalore.nf

@@ -224,6 +224,7 @@ workflow RNASEQ {
         ch_cat_fastq,
         params.skip_fastqc || params.skip_qc,
         params.with_umi,
+        params.skip_umi_extract,
         params.skip_trimming,
         params.umi_discard_read
     )