tourmaline

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Provide conda environments as YAML files

1

Export conda environments (Mac, Linux) and share on GitHub. M1 and Intel both needed?

lukenoaa

Add utility scrips to check that primers/adapters removed

2

lukenoaa

Jon Sanders has database/solution for testing.

lukenoaa

For systems that don't have Docker due to cost or security reasons

lukenoaa

https://docs.github.com/en/repositories/releasing-projects-on-github/managing-releases-in-a-repository

lukenoaa

Need a new rule.

lukenoaa

Need a new rule.

lukenoaa

Fragment insertion (SEPP) in addition to de novo tree.

lukenoaa

Rule not working properly: ``` # mac: md5 / linux: md5sum rule check_repseq_md5: input: "02-output-{method}/00-table-repseqs/representative_sequences.fasta" output: "02-output-{method}/00-table-repseqs/representative_sequences_md5_status.txt" shell: "seq1id=`head -n 1 {input} | sed 's/^>//'`; " "seq1md5=`head -n 2 {input}...

lukenoaa

User-provided file path for reference database/classifier

1

Change from refseqs.qza/reftax.qza or classifier.qza to a user-provided file path (alt: Opal provides file path on server) See how Opal handles this here: https://github.com/Geo-omics/GLAMR_omics_pipelines/blob/adc9f8ca09c68e1b7948669a5163fa40fb873551/Snakefile#L319 @ksilnoaa @CarterRoll @baydenwillms

lukenoaa