Merge pull request #410 from nf-core/409-cellranger-multi-fails-witho…

…ut---fb_reference-even-if-not-needed
nf-core · Dec 29, 2024 · 1fc15e9 · 1fc15e9
2 parents 68d2811 + 0d6d083
commit 1fc15e9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## dev
+
+- Add a checker so that `--fb_reference` does not break the pipeline in case `ab` files are not used in `cellranger multi` sub-workflow.
+
 ## v3.0.0 - 2024-12-09
 
 ## Backwards-incompatible changes

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,7 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/3.0.0" target="_blank">nf-core/scrnaseq</a>
-  analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/scrnaseq/3.0.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/tree/dev" target="_blank">nf-core/scrnaseq</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/scrnaseq/dev/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

diff --git a/nextflow.config b/nextflow.config
@@ -287,7 +287,7 @@ manifest {
     description     = """Pipeline for processing 10x Genomics single cell rnaseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '3.0.0'
+    version         = 'dev'
     doi             = '10.5281/zenodo.3568187'
 }
 

diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf
@@ -43,7 +43,7 @@ workflow CELLRANGER_MULTI_ALIGN {
                 vdj: meta.feature_type == "vdj"
                     return [ meta, fastq ]
                 ab: meta.feature_type == "ab"
-                    if (params.fb_reference){
+                    if ((fastq == file("$projectDir/assets/EMPTY", checkIfExists: true)) || params.fb_reference) { // when empty, should not check for reference
                         return [ meta, fastq ]
                     } else {
                         error ("Antibody reference was not specified. Please provide a reference file for feature barcoding (e.g. antibody measurements).\nPlease refer to https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-feature-ref-csv for more details.")