Add DIAMOND blastp subworkflow for protein homology search against NCBI RefSeq - #50

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tracelail wants to merge 67 commits into

nf-core:devfrom

tracelail:unfinished-diamond-blastp

Commits on Mar 26, 2025

Install diamond/blastp
eweizy
committed
53aa47c
Unfinished diamond/blastp integraton
eweizy
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55b7632
Add diamond
eweizy
committed
3c5b661

Commits on May 21, 2025

reinstalled diamond/blastp module. Installed blast/makeblastdb
tracelail
committed
b1fdc74

Commits on Jun 2, 2025

wrote draft integration of BLAST_MAKEBLASTDB and NCBIREFSEQDOWNLOAD into functional_annotation subworkflow.
tracelail
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9f1ea67

Commits on Jun 10, 2025

removed blast/makeblastdb nf-core module and create local diamondpreparetaxa local module template.
tracelail
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f12c619

Commits on Jun 17, 2025

finished up writing the ncbirefseqdownload process for the first draft and wrote an initial main.nf.test for the process
tracelail
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4f4db82

Commits on Jun 18, 2025

edited ncbirefseqdownload script to a working stated where the nf-test process is successful.
tracelail
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3946ba5

Commits on Jun 26, 2025

created a working ncbirefseqdownload module with basic nf-test. Also utilized tests/nextflow.config to fix memory error.
tracelail
committed
94ebe1b

Commits on Jun 27, 2025

added more working tests to ncbirefseqdownload and organized.
tracelail
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06bf5e8

Commits on Jun 30, 2025

Added diamondpreparetaxa main.nf script and a process.success nf-test.
tracelail
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7681f82

Commits on Jul 1, 2025

Merge branch 'dev' into unfinished-diamond-blastp
tracelail
authored
0cf27f7

Commits on Jul 2, 2025

added working snapshot assertions for process.out match and versions to diamondpreparetaxa module
tracelail
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92c847c

Commits on Jul 7, 2025

Added output documentation for all seven Diamond subworkflow outputs.
tracelail
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043451f

Commits on Jul 9, 2025

Commits on Jul 28, 2025

Apply suggestions from code review

tracelail
and
olgabot
authored
4eb5ad1

Commits on Jul 29, 2025

Commits on Jul 30, 2025

corrected typo in diamondpreparetaxa container
tracelail
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c970041
updated diamond/makedb module
tracelail
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925ed89

Commits on Jul 31, 2025

Commits on Aug 6, 2025

working subworkflow nf-test with large prot.accession2taxid.gz taxonmap.
tracelail
committed
8edc405

Commits on Aug 7, 2025

Updated diamond subworkflow main.nf.test with a smaller taxonmap for testing
tracelail
committed
a3e661c

Commits on Aug 21, 2025

created a local diamond subworkflow that produces a diamond/blastp output
tracelail
committed
3fbcc6a

Commits on Oct 2, 2025

Commits on Oct 3, 2025

Commits on Mar 30, 2026

Commits on Mar 31, 2026

updated missed merge conflict
tracelail
committed
4dcba98

Commits on Apr 3, 2026

Commits on Apr 6, 2026

Commits on Apr 9, 2026

Commits on Aug 18, 2026

Commits on Aug 20, 2026

updated ncbi download to use rclone since rsync is depricated by ncbi. Updated meta and environment to match. snap needs pruning once ncbi real test can run after ban.
tracelail
committed
5ba47b3

Commits on Aug 21, 2026

restored domain_annotation via git checkout dev.
tracelail
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b0da026
updated modules.config
tracelail
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5dee8c0
Added skip_diamond functionality to pipeline and ran stub tests.
tracelail
committed
e204f10

Commits on Aug 26, 2026