Merge pull request #97 from sanger-tol/draft_assemblies

Support draft assemblies

Author: muffato

CHANGELOG.md

@@ -3,6 +3,45 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## – Bellsprout – []
+
+The pipeline has now been validated for draft (unpublished) assemblies.
+
+- The pipeline now queries the NCBI database instead of GoaT to establish the
+  taxonomic classification of the species and the relevant Busco lineages.
+  In case the taxon_id is not found, the pipeline falls back to GoaT, which
+  is aware of upcoming taxon_ids in ENA.
+- New `--busco_lineages` parameter to choose specific Busco lineages instead of
+  automatically selecting based on the taxonomy.
+- All parameters are now passed the regular Nextflow way. There is no support
+  for the original Yaml configuration files of the Snakemake version.
+- New option `--skip_taxon_filtering` to skip the taxon filtering in blast searches.
+  Mostly relevant for draft assemblies.
+
+### Parameters
+
+| Old parameter | New parameter          |
+| ------------- | ---------------------- |
+| --yaml        |                        |
+|               | --busco_lineages       |
+|               | --skip_taxon_filtering |
+
+> **NB:** Parameter has been **updated** if both old and new parameter information is present. </br> **NB:** Parameter has been **added** if just the new parameter information is present. </br> **NB:** Parameter has been **removed** if new parameter information isn't present.
+
+### Software dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own [Biocontainer](https://biocontainers.pro/#/registry). This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference. Only `Docker` or `Singularity` containers are supported, `conda` is not supported.
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| goat       | 0.2.5       |             |
+
+## [[0.5.1](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.5.1)] – Snorlax (patch 1) – [2024-08-22]
+
+### Enhancements & fixes
+
+- Bugfix: skip BLASTN if there are no chunks to align
+
 ## [[0.5.0](https://github.com/sanger-tol/blobtoolkit/releases/tag/0.5.0)] – Snorlax – [2024-07-31]
 
 General tidy up of the configuration and the pipeline

README.md

@@ -16,7 +16,7 @@ It takes a samplesheet of BAM/CRAM/FASTQ/FASTA files as input, calculates genome
 
 1. Calculate genome statistics in windows ([`fastawindows`](https://github.com/tolkit/fasta_windows))
 2. Calculate Coverage ([`blobtk/depth`](https://github.com/blobtoolkit/blobtk))
-3. Fetch associated BUSCO lineages ([`goat/taxonsearch`](https://github.com/genomehubs/goat-cli))
+3. Determine the appropriate BUSCO lineages from the taxonomy.
 4. Run BUSCO ([`busco`](https://busco.ezlab.org/))
 5. Extract BUSCO genes ([`blobtoolkit/extractbuscos`](https://github.com/blobtoolkit/blobtoolkit))
 6. Run Diamond BLASTp against extracted BUSCO genes ([`diamond/blastp`](https://github.com/bbuchfink/diamond))

assets/mapping_taxids-busco_dataset_name.2019-12-16.txt

@@ -0,0 +1,166 @@
+422676	aconoidasida
+7898	actinopterygii
+5338	agaricales
+155619	agaricomycetes
+33630	alveolata
+5794	apicomplexa
+6854	arachnida
+6656	arthropoda
+4890	ascomycota
+8782	aves
+5204	basidiomycota
+68889	boletales
+3699	brassicales
+134362	capnodiales
+33554	carnivora
+91561	cetartiodactyla
+34395	chaetothyriales
+3041	chlorophyta
+5796	coccidia
+28738	cyprinodontiformes
+7147	diptera
+147541	dothideomycetes
+3193	embryophyta
+33392	endopterygota
+314146	euarchontoglires
+33682	euglenozoa
+2759	eukaryota
+5042	eurotiales
+147545	eurotiomycetes
+9347	eutheria
+72025	fabales
+4751	fungi
+314147	glires
+1028384	glomerellales
+5178	helotiales
+7524	hemiptera
+7399	hymenoptera
+5125	hypocreales
+50557	insecta
+314145	laurasiatheria
+147548	leotiomycetes
+7088	lepidoptera
+4447	liliopsida
+40674	mammalia
+33208	metazoa
+6029	microsporidia
+6447	mollusca
+4827	mucorales
+1913637	mucoromycota
+6231	nematoda
+33183	onygenales
+9126	passeriformes
+5820	plasmodium
+92860	pleosporales
+38820	poales
+5303	polyporales
+9443	primates
+4891	saccharomycetes
+8457	sauropsida
+4069	solanales
+147550	sordariomycetes
+33634	stramenopiles
+32523	tetrapoda
+155616	tremellomycetes
+7742	vertebrata
+33090	viridiplantae
+71240	eudicots
+57723	acidobacteria
+201174	actinobacteria_phylum
+1760	actinobacteria_class
+28211	alphaproteobacteria
+135622	alteromonadales
+200783	aquificae
+1385	bacillales
+91061	bacilli
+2	bacteria
+171549	bacteroidales
+976	bacteroidetes
+68336	bacteroidetes-chlorobi_group
+200643	bacteroidia
+28216	betaproteobacteria
+80840	burkholderiales
+213849	campylobacterales
+1706369	cellvibrionales
+204428	chlamydiae
+1090	chlorobi
+200795	chloroflexi
+135613	chromatiales
+1118	chroococcales
+186801	clostridia
+186802	clostridiales
+84999	coriobacteriales
+84998	coriobacteriia
+85007	corynebacteriales
+1117	cyanobacteria
+768507	cytophagales
+768503	cytophagia
+68525	delta-epsilon-subdivisions
+28221	deltaproteobacteria
+213118	desulfobacterales
+213115	desulfovibrionales
+69541	desulfuromonadales
+91347	enterobacterales
+186328	entomoplasmatales
+29547	epsilonproteobacteria
+1239	firmicutes
+200644	flavobacteriales
+117743	flavobacteriia
+32066	fusobacteria
+203491	fusobacteriales
+1236	gammaproteobacteria
+186826	lactobacillales
+118969	legionellales
+85006	micrococcales
+31969	mollicutes
+2085	mycoplasmatales
+206351	neisseriales
+32003	nitrosomonadales
+1161	nostocales
+135619	oceanospirillales
+1150	oscillatoriales
+135625	pasteurellales
+203682	planctomycetes
+85009	propionibacteriales
+1224	proteobacteria
+72274	pseudomonadales
+356	rhizobiales
+227290	rhizobium-agrobacterium_group
+204455	rhodobacterales
+204441	rhodospirillales
+766	rickettsiales
+909929	selenomonadales
+117747	sphingobacteriia
+204457	sphingomonadales
+136	spirochaetales
+203691	spirochaetes
+203692	spirochaetia
+85011	streptomycetales
+85012	streptosporangiales
+1890424	synechococcales
+508458	synergistetes
+544448	tenericutes
+68295	thermoanaerobacterales
+200918	thermotogae
+72273	thiotrichales
+1737405	tissierellales
+1737404	tissierellia
+74201	verrucomicrobia
+135623	vibrionales
+135614	xanthomonadales
+2157	archaea
+2266	thermoproteales
+2281	sulfolobales
+114380	desulfurococcales
+183967	thermoplasmata
+651137	thaumarchaeota
+2182	methanococcales
+2191	methanomicrobiales
+183925	methanobacteria
+183924	thermoprotei
+2235	halobacteriales
+1644060	natrialbales
+224756	methanomicrobia
+1644055	haloferacales
+183963	halobacteria
+28890	euryarchaeota