"--gtf_extra_attributes" only works by giving one attribute and not comma separated multiple values

[ahwanpandey]

Description of the bug

Hi,

The --gtf_extra_attributes only works when you give it one extra attribute. Eg.. --gtf_extra_attributes gene_name works whereas --gtf_extra_attributes gene_name,gene_type does not work. The following is the output in tx2gene.tsv

The usage section seems to relay that multiple attributes should work:

Here are are a couple of lines from my GENCODE GTF:

chr1    HAVANA  transcript      11121   14413   .       +       .       gene_id "ENSG00000290825.2"; transcript_id "ENST00000832824.1"; gene_type "lncRNA"; gene_name "DDX11L16"; transcript_type "lncRNA"; transcript_name "DDX11L16-260"; level 2; tag "TAGENE";
chr1    HAVANA  exon    11121   11211   .       +       .       gene_id "ENSG00000290825.2"; transcript_id "ENST00000832824.1"; gene_type "lncRNA"; gene_name "DDX11L16"; transcript_type "lncRNA"; transcript_name "DDX11L16-260"; exon_number 1; exon_id "ENSE00004248723.1"; level 2; tag "TAGENE";
chr1    HAVANA  exon    12010   12227   .       +       .       gene_id "ENSG00000290825.2"; transcript_id "ENST00000832824.1"; gene_type "lncRNA"; gene_name "DDX11L16"; transcript_type "lncRNA"; transcript_name "DDX11L16-260"; exon_number 2; exon_id "ENSE00004248735.1"; level 2; tag "TAGENE";

Also, v3.21.0 still seems to use --featurecounts_group_type and not --gtf_group_features_type as mentioned in the usage:

Thanks,
Ahwan

Command used and terminal output

nextflow run $NEXTFLOW_PIPELINE_DIR \
-profile singularity \
-c $CLUSTER_CONFIG_FILE \
-params-file $PARAMS_FILE

params file and nextflow log attached below

Relevant files

nextflow.log

nfcore_params.json

System information

Nextflow version (v24.10.5)
Hardware (HPC)
Executor (slurm)
Container engine: (singularity)
OS (Redhat)
Version of nf-core/rnaseq (v3.21.0)

[ahwanpandey]

@pinin4fjords I just pulled v3.22.1 and there is an issue with the salmon quantification files. I am running the exact same command that was working previously with v3.21.0 when I initially created this github issue.

Previously, you can see that the gene counts tables had the gene counts (file-sizes were smaller) and the transcript counts tables had the transcript counts (file-sizes were bigger)

contents of the "salmon.merged.gene_counts.tsv" file in v3.21.0 which is correct

But with v3.22.1, the "salmon.merged.gene_counts.tsv" is not counting genes but transcripts. The two files "salmon.merged.gene_counts.tsv" and "salmon.merged.transcript_counts.tsv" both have transcript level results.

contents of the "salmon.merged.gene_counts.tsv" file in v3.22.1 which is not correct

[pinin4fjords]

@ahwanpandey I think I see the issue, I've put a fix in the modules repo nf-core/modules#9520.

Could you try installing that version for me and making sure the fix is good before I merge?:

nf-core modules --branch  fix/tximport-extra-columns update tximeta/tximport