# The catalogue of analysis modules that can be installed. # # `PoolSeqFlow analysis modules available` and `... modules install ` read this file over # the network, from the repository's default branch. It is NOT part of a release download: # .gitattributes export-ignores it, so a tarball carries no copy that could disagree with the # published one. That is the whole point - a module is published on its own timetable, and the # release it is installed into does not change when one appears. # # One row per published module VERSION, tab-separated. Several rows may name one module; the # newest version whose contract this release speaks is what `install ` picks, and naming a # version installs exactly that one. # # name the module's name, which is also the directory it installs into # version its own version, independent of any pipeline release # contract the published-table contract it reads. This release speaks the one # analysis/modules.nf returns from contractVersion() # frame the oldest analysis/frame.version it runs on, YYYYMMDD.NNN. Copy it from the # module's own manifest; a row that leaves it empty is treated as no requirement # environment the oldest PoolSeqFlow release whose analysis environment holds what it needs, # X.Y.Z, likewise copied from the manifest # url where the tarball is, unpacking to / with manifest.json and main.nf in it # sha256 the tarball's checksum, which install verifies before unpacking anything # summary one line, shown by `modules available` # # `frame` and `environment` are what let one catalogue serve several releases at once. Publish a # row per version and `install ` takes the newest one THIS release can actually run, # rather than the newest one that exists and then failing when it is first used. They repeat # what the module's manifest already says, because the choice has to be made before the tarball # is downloaded. # # THE COLUMNS ARE READ BY NAME, out of the header row below, so their order here does not # matter and a column a release has never heard of is ignored rather than misread. Adding one # later is therefore safe and needs no layout bump - which is the whole reason to add a column # rather than overload an existing one. # # Adding a module is adding a row. Removing one takes it out of `available` and leaves every # installation that already has it untouched. # # THE TWO VERSIONS BELOW DO DIFFERENT JOBS AND ARE NOT INTERCHANGEABLE. # # index-format is the COLUMN LAYOUT, and every wrapper checks it before reading a single row. # Since the columns are matched by name it is NOT bumped for a new one - that is additive and # every older release simply ignores it. It is for a change that cannot be read at all: a # required column renamed or removed, or one whose meaning changed under the same name. Bumping # it stops every already-published release from reading this file, so it is close to a last # resort. # # index-version is WHAT IS IN THE CATALOGUE, in the same YYYYMMDD.NNN form the frame and the # modules use. Bump it on every publish. Nothing is refused on it - a release must be able to # read a catalogue newer than itself, which is the whole point of publishing modules # separately - so it is reported and recorded, never compared. # #!index-format: 1 #!index-version: 20260910.011 name kind version contract frame environment url sha256 summary basicstats module 20260910.001 freq-1 20260908.003 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/basicstats-20260910.001.tar.gz f154f07cbcc66abab0b330fb1a4d0ce55dfd7db0625d37f9840e6d083039883b site counts, depth, effective pool size and gene diversity, per pool association module 20260910.001 freq-1 20260908.003 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/association-20260910.001.tar.gz 19b68feb0ca7879143e88b2a6e206b663e7d1bb9935d1e98fa42dcbdc7704913 each allele's frequency regressed on a phenotype measured per pool, with a permutation p mds module 20260910.001 freq-1 20260908.003 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/mds-20260910.001.tar.gz 96797656267316ff5971981c8d940ab6ddc1fa34800eed6312a1c7ded1d5facf the pools placed by Nei's minimum distance, on a classical MDS (principal coordinates analysis) n_eff library 20260910.002 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/n_eff-20260910.002.tar.gz 2e00ba744d822fa0757b0420633933c5363dc789522fe38e0dd55de14994c671 effective pool size at a site and over a pool, and the harmonic mean it needs chunk_ranges library 20260910.002 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/chunk_ranges-20260910.002.tar.gz f07ff963e7bc1bf18a00f11ac94c2b8d43e9d0bcc9b960bf2a0977e83257d707 a row count split into contiguous bins for chunked or parallel reading allele_frequencies library 20260910.002 freq-1 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/allele_frequencies-20260910.002.tar.gz 5acc9666a1252dd30af0d679a259a380f21848bb618fb7e8bcc769a12a1e080e per-site allele frequencies parsed from the depth table, vectorized R with a compiled path site_diversity library 20260910.002 freq-1 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/site_diversity-20260910.002.tar.gz 2f29207471cb902d8e763b19279089d3ce6cbf50643e734af34734486bfe0e0b gene diversity per site, 1 - sum(p^2), vectorized R with a compiled path nei_distance library 20260910.002 freq-1 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/nei_distance-20260910.002.tar.gz 219267582b965264f72dc9cf34e6c8260c23db4c0063cc1c9dd8d7d3ce44bdfd Nei's minimum distance accumulated over sites, combined and averaged, with a compiled path basicstats module 20260910.004 freq-1 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/basicstats-20260910.004.tar.gz 629b80eb87cb6d5c02fe5f0b41f2a5e912aa982c18d86f624b196f29d0e857c1 site counts, depth, effective pool size and gene diversity, per pool association module 20260910.004 freq-1 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/association-20260910.004.tar.gz 7e38083b9f43077e947cf34ab8b30f31050e8e5997b2b5cc06bdf8c3d04660c7 each allele's frequency regressed on a phenotype measured per pool, with a permutation p mds module 20260910.003 freq-1 20260910.001 3.0.0 https://ozankiratli.github.io/PoolSeqFlow/modules-repo/mds-20260910.003.tar.gz 0a3754b917e560921de2c835d2469520664b93105a5a2af13ea44f51a095299a the pools placed by Nei's minimum distance, on a classical MDS (principal coordinates analysis)