External Data

Tourmaline 2 can start steps from externally generated inputs when provided as QIIME 2 artifacts with the expected types.

Repseqs step: external demultiplexed sequences

Provide a QIIME 2 artifact of demultiplexed sequences:

# in config_02_repseqs.yaml
fastq_qza_file: /abs/path/to/fastq.qza

Or reuse QA/QC outputs by specifying qaqc_run_name.

Taxonomy step: external repseqs and table

Provide both files:

# in config_03_taxonomy.yaml
repseqs_qza_file: /abs/path/to/repseqs.qza
table_qza_file: /abs/path/to/table.qza

Conversions

Convert FASTA to QZA (ASV sequences):

qiime tools import \
   --type 'FeatureData[Sequence]' \
   --input-path my-asvs.fasta \
   --output-path output-asvs.qza

Convert BIOM v2.1 to QZA (feature table):

qiime tools import \
  --input-path feature-table-v210.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path feature-table.qza

If starting from a TSV count table, first convert to BIOM (see BIOM docs), then import.