Input file name collision on 'annotate:write_gff'

[FabioPossebon]

Hi! I am trying to run the pipeline for 12 samples, with the following parameters:

nextflow run EBI-Metagenomics/emg-viral-pipeline --fasta "./contigs_rnaSpades/*.fasta" --cores 8 -profile local,docker -w work --databases databases/ --length 2.0

It goes to every process until 'annotate:write_gff', when this error is shown:

ERROR ~ Error executing process > 'annotate:write_gff'

Caused by: Process annotate:write_gff input file name collision -- There are multiple input files for each of the following file names: low_confidence_viral_contigs_prodigal_annotation_taxonomy.tsv, low_confidence_viral_contigs_prodigal_annotation.tsv, low_confidence_viral_contigs_quality_summary.tsv, prophages_quality_summary.tsv, high_confidence_viral_contigs_quality_summary.tsv

Is there any solution for this? Thank you a lot!

[mberacochea]

Hi @FabioPossebon

he pipeline doesn't support multiple input fasta files, you will have to lunch multiples instances of the pipeline (one per assembly)

Cheers

[hoelzer]

Maybe it helps to try

nextflow run EBI-Metagenomics/emg-viral-pipeline --fasta './contigs_rnaSpades/*.fasta' --cores 8 -profile local,docker -w work --databases databases/ --length 2.0 

Attention, the difference is

'./contigs_rnaSpades/*.fasta'

instead of

"./contigs_rnaSpades/*.fasta"

Then, the pipeline should run and span multiple processes for the different FASTA files.