Additional fasta with GENCODE annotation results in biotype error

[j-andrews7]

Description of the bug

Passing an additional FASTA to add to an annotation (e.g. ERCC spike-ins) results in their "type" in the resulting GTF to be set as "gene_biotype". This is an issue when using a GENCODE annotation and the biotype QC, as their --featurecounts_group_type is "gene_type".

Steps to reproduce

Run with a GENCODE annotation file and provide an additional fasta. Set --featurecounts_group_type "gene_type". This results in an error as follows:

//================================= Running ==================================\\
  ||                                                                            ||
  || Load annotation file HG19_ERCC92.gtf ...                                   ||
  
  ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
  The specified gene identifier attribute is 'gene_type' 
  An example of attributes included in your GTF annotation is 'exon_id "ERCC-00002.1"; exon_number "1"; gene_biotype "transgene"; gene_id "ERCC-00002_gene"; gene_name "ERCC-00002_gene"; gene_source "custom"; transcript_id "ERCC-00002_gene"; transcript_name "ERCC-00002_gene";' 
  The program has to terminate.

Expected behaviour

The ideal behavior would be to set the gene_biotype field to gene_type during the GTF building step if the --encode flag is provided.

System

• Hardware: HPC
• Executor: lsf

Container engine

• Engine: singularity
• version: dev (v3.1)
• Image tag: nfcore/rnaseq:dev

[cutleraging]

Sorry to re-open this but I am having a similar issue. The difference is that I am not using a gencode annotation.

Command:

$ nextflow run nf-core/rnaseq \
-r 3.9 \
-profile singularity \
--outdir /gs/gsfs0/users/vijg-lab/2022-Ronnie/DNA-RNA_ERCC_test/sequencing/3_nf-core-rnaseq_ERCC \
--input samplesheet.csv \
--email ronald.cutler@einsteinmed.edu \
--with_umi FALSE \
--genome GRCh38 \
--aligner star_rsem \
--save_unaligned TRUE \
--max_cpus 16 \
--max_memory 128.GB \
--additional_fasta /gs/gsfs0/users/rcutler/References/ERCC92.fa \
--save_reference TRUE

Error:

//================================= Running ==================================\\
 ||                                                                            ||
 || Load annotation file GRCh38_ERCC92.gtf ...                                 ||
 
 ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file.
 The specified gene identifier attribute is 'gene_biotype' 
 An example of attributes included in your GTF annotation is 'gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "rna0"; tss_id "TSS31672";' 
 The program has to terminate.