I ran with the following input yaml file

- genome: GRCh38.p14
  fasta: <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GRCh38_major_release_seqs_for_alignment_pipelines/GCA_000001405.15_GRCh38_full_analysis_set.fna.gz>
  gff: <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gff.gz>
  gtf: <https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.40_GRCh38.p14/GCF_000001405.40_GRCh38.p14_genomic.gtf.gz>
  mito_name: MT
  source_version: GCF_000001405.40
  source: NCBI
  species: Homo_sapiens

and

--tools bwamem1,createsequencedictionary,dragmap,faidx,intervals,rsem,rsem_make_transcript_fasta,salmon,sizes,star,tabix

, which kinda worked, although rsem/star were unhappy with the GFF/GTF files. Are there any examples of putting together multiple sources into one input yaml file? I'm thinking specifically GRCh38.p14 plus GATK bundle for sarek and Ensembl and Encode for rnaseq rsem/star.