Easy fix for #754

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 * [[#744](https://github.com/nf-core/rnaseq/issues/744)] - Auto-detect and raise error if CSI is required for BAM indexing
 * [[#752](https://github.com/nf-core/rnaseq/issues/752)] - How to set publishing mode for all processes?
 * [[#753](https://github.com/nf-core/rnaseq/issues/753)] - Add warning when user provides `--transcript_fasta`
+* [[#754](https://github.com/nf-core/rnaseq/issues/754)] - DESeq2 QC issue linked to `--count_col` parameter
 * [[#755](https://github.com/nf-core/rnaseq/issues/755)] - Rename RSEM_PREPAREREFERENCE_TRANSCRIPTS process
 * [[#759](https://github.com/nf-core/rnaseq/issues/759)] - Empty lines in samplesheet.csv cause a crash
 

bin/deseq2_qc.r

@@ -30,7 +30,7 @@ library(pheatmap)
 
 option_list <- list(
     make_option(c("-i", "--count_file"    ), type="character", default=NULL    , metavar="path"   , help="Count file matrix where rows are genes and columns are samples."                        ),
-    make_option(c("-f", "--count_col"     ), type="integer"  , default=2       , metavar="integer", help="First column containing sample count data."                                             ),
+    make_option(c("-f", "--count_col"     ), type="integer"  , default=3       , metavar="integer", help="First column containing sample count data."                                             ),
     make_option(c("-d", "--id_col"        ), type="integer"  , default=1       , metavar="integer", help="Column containing identifiers to be used."                                              ),
     make_option(c("-r", "--sample_suffix" ), type="character", default=''      , metavar="string" , help="Suffix to remove after sample name in columns e.g. '.rmDup.bam' if 'DRUG_R1.rmDup.bam'."),
     make_option(c("-o", "--outdir"        ), type="character", default='./'    , metavar="path"   , help="Output directory."                                                                      ),