add contextual fasta input for augur_from_assemblies (#558)

* add contextual_genome_fastas input for auger_from_assemblies workflow

add contextual_genome_fastas input for auger_from_assemblies workflow, so contextual genomes can be provided from a different source than the assembly_fastas (the two inputs are ultimately merged into one prior to alignment)

pipes/WDL/workflows/augur_from_assemblies.wdl

@@ -13,6 +13,7 @@ workflow augur_from_assemblies {
 
  input {
  Array[File]+ assembly_fastas
+ Array[File]? contextual_genome_fastas
  Array[File]+ sample_metadata_tsvs
  File ref_fasta
 
@@ -29,6 +30,10 @@ workflow augur_from_assemblies {
  description: "Set of assembled genomes to align and build trees. These must represent a single chromosome/segment of a genome only. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture.",
  patterns: ["*.fasta", "*.fa", "*.fasta.gz", "*.fasta.zst"]
  }
+ contextual_genome_fastas: {
+ description: "Set of near-complete contextual genomes to include in tree build. Each fasta provided must represent a single chromosome/segment of a genome. Fastas may be one-sequence-per-individual or a concatenated multi-fasta (unaligned) or a mixture of the two. They may be compressed (gz, bz2, zst, lz4), uncompressed, or a mixture. ",
+ patterns: ["*.fasta", "*.fa", "*.fasta.gz", "*.fasta.zst"]
+ }
  sample_metadata_tsvs: {
  description: "Tab-separated metadata file that contain binning variables and values. Must contain all samples: output will be filtered to the IDs present in this file.",
  patterns: ["*.txt", "*.tsv"]
@@ -54,7 +59,7 @@ workflow augur_from_assemblies {
 
  call utils.zcat {
  input:
- infiles = assembly_fastas,
+ infiles = flatten([assembly_fastas, select_first([contextual_genome_fastas,[]])]),
  output_name = "all_samples_combined_assembly.fasta"
  }
  call utils.filter_sequences_by_length {