fix issue with merge_UMI

mapo9 · Jul 17, 2024 · cfa4f73 · cfa4f73
1 parent b8dc66e
commit cfa4f73
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Showing 3 changed files with 6 additions and 8 deletions.
diff --git a/docs/usage.md b/docs/usage.md
@@ -177,7 +177,7 @@ It is possible to provide several fastq files per sample (e.g. sequenced over di
 ### Fastq input samplesheet (untargeted bulk or sc RNA sequencing)
 
 When running the untargeted protocol, BCR or TCR sequences will be extracted from the untargeted bulk or single-cell RNA sequencing with tools such as [TRUST4](https://github.com/liulab-dfci/TRUST4).
-The required input file is the same as for the [Fastq bulk AIRR samplesheet](#fastq-input-samplesheet-bulk-airr-sequencing).
+The required input file is the same as for the [Fastq bulk AIRR samplesheet](#fastq-input-samplesheet-bulk-airr-sequencing) or [Fastq single-cell AIRR samplesheet](#fastq-input-samplesheet-single-cell-sequencing) depending on the input data type (bulk RNAseq or single-cell RNAseq).
 
 ### Assembled input samplesheet (bulk or single-cell sequencing)
 

diff --git a/subworkflows/local/fastq_input_check.nf b/subworkflows/local/fastq_input_check.nf
@@ -84,13 +84,11 @@ def create_fastq_channels(LinkedHashMap col) {
             error "ERROR: Please check input samplesheet -> Index read FastQ file does not exist!\n${col.filename_I1}"
         }
         array = [ meta, [ file(col.filename_R1), file(col.filename_R2), file(col.filename_I1) ] ]
-    }
-    if (params.library_generation_method == "trust4") {
-        meta.barcode_read = params.barcode_read
-        meta.umi_read = params.umi_read
-        array = [ meta, [ file(col.filename_R1), file(col.filename_R2) ] ]
     } else {
         array = [ meta, [ file(col.filename_R1), file(col.filename_R2) ] ]
+        if (params.index_file) {
+            error "ERROR: Index file path was provided but the index file path is not specified in the samplesheet!"
+        }
     }
     return array
 }
diff --git a/subworkflows/local/rnaseq_input.nf b/subworkflows/local/rnaseq_input.nf
@@ -79,8 +79,8 @@ workflow RNASEQ_INPUT {
     ch_reads_trust4.dump(tag: "trust4_input")
 
     // create barcode and umi channels for nf-core trust4 module
-    barcode_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 ->  [meta, meta.barcode_read] }
-    umi_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 -> [meta, meta.umi_read] }
+    barcode_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 ->  [meta, params.barcode_read] }
+    umi_channel = ch_reads_fastp_filtered.map { meta, read_1, read_2 -> [meta, params.umi_read] }
 
     TRUST4(
         ch_reads_trust4,