Hey, I was using this option in MAG: spades_downstreaminput = 'contigs' and while launching the pipeline it shows this as valid parameter: Assembly options spades_downstreaminput : contigs skip_megahit : true skip_metamdbg : true skip_flye : true However in downstream process like BOWTIE2_ASSEMBLY_BUILD, Binning and DAS tools, it uses scaffolds instead of contigs. As I can see in logs: usr/local/bin/quast.py --threads 1 --rna-finding SPAdes-03_D17_S13.scaffolds.fa -o /lustre/rsharma/animal_gut_MAGs/workdir/71/5233237b209d875457b4be9a86b941/QUAST --labels SPAdes-03_D17_S13 DAS Tool 1.1.7 2026-02-05 202326.46999 Parameters: --bins SPAdes-MaxBin2-SP62_D17_S28.tsv,SPAdes-CONCOCT-SP62_D17_S28.tsv,SPAdes-MetaBAT2-SP62_D17_S28.tsv --contigs SPAdes-SP62_D17_S28.scaffolds.fa --outputbasename SPAdes-DASTool-SP62_D17_S28

Ooof, it looks like that bit of code got lost during the refactoring of the assembling steps into subworkflows 🫥