message: increase tree size
diff: @@ -11,11 +11,39 @@ builds:
  custom_rules:
  - nextstrain_profiles/nextstrain/subsampling_ranges.smk
  - - nextstrain_profiles/nextstrain/download_preprocessed.smk
  title: 'Your samples placed on a SARS-CoV-2 phylogeny'
  -S3_BUCKET: "nextstrain-ncov-private"
  +# These parameters are only used by the `export_for_nextstrain` rule and shouldn't need to be modified.
  +# To modify the s3 _source_ bucket, specify this directly in the `inputs` section of the config.
  +# P.S. These are intentionally set as top-level keys as this allows command-line overrides.
  +S3_DST_BUCKET: "nextstrain-ncov-private"
  +S3_DST_COMPRESSION: "xz"
  +S3_DST_ORIGINS: ["gisaid"]
  +
  +genes: ["ORF1a", "ORF1b", "S", "ORF3a", "M", "N"]
  +use_nextalign: true
  +
  +# NOTE for shepherds -- there are commented out inputs here, you can
  +# uncomment them to start the pipeline at that stage.
  +# E.g. if you uncomment `filtered` then the pipeline
  +# will start by downloading that file and proceeding straight to
  +# subsampling
  +inputs:
  + - name: gisaid
  + metadata: "s3://nextstrain-ncov-private/metadata.tsv.gz"
  + sequences: "s3://nextstrain-ncov-private/sequences.fasta.gz"
  + # ---------------------- NOTE --------------------------
  + # PR 550 changed the path of intermediate files on
  + # the S3 bucket to include the origin (e.g. _gisaid).
  + # Some of these files may not yet exist!
  + # ------------------------------------------------------
  + # metadata: "s3://nextstrain-ncov-private/metadata_gisaid.tsv.gz"
  + # sequences: "s3://nextstrain-ncov-private/sequences_gisaid.fasta.gz"
  + # aligned: "s3://nextstrain-ncov-private/aligned_gisaid.fasta.xz"
  + # to-exclude: "s3://nextstrain-ncov-private/to-exclude_gisaid.txt.xz"
  + # masked: "s3://nextstrain-ncov-private/masked_gisaid.fasta.fasta.xz"
  + # filtered: "s3://nextstrain-ncov-private/filtered_gisaid.fasta.xz"
  filter:
  min_length: 28500
  @@ -36,7 +64,7 @@ subsampling:
  nextclade:
  global_late:
  group_by: 'country year month'
  - max_sequences: 1000
  + max_sequences: 1500
  global_early:
  group_by: 'region year month'
  max_sequences: 500
  