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…ent identity parameters, and why
Co-authored-by: James A. Fellows Yates <[email protected]>
Document percent identity parameters
Optmise full test resources for AWS megatest
Add binner COMEBin
Important! Template update for nf-core/tools v3.4.1
Change name from willros to William Rosenbaum in README
Co-authored-by: James A. Fellows Yates <[email protected]>
Only error on bin length filter if there are bins
Version bump for 5.1.0 release
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jonasscheid
approved these changes
Oct 25, 2025
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LGTM! Only one (optional) nitpick. Maybe also check on the diff in versions for the one failing conda test (I know it's annoying)
97 "GENOMAD_DOWNLOAD": { 97 "GENOMAD_DOWNLOAD": {
! 98 "genomad": "1.11.0" ! 98 "genomad": "1.9.4"
99 }, 99 },
100 "GENOMAD_ENDTOEND": { 100 "GENOMAD_ENDTOEND": {
! 101 "genomad": "1.11.0" ! 101 "genomad": "1.9.4"
102 }, 102 }, | - (optionally) performs ancient DNA assembly validation using [PyDamage](https://github.com/maxibor/pydamage) and contig consensus sequence recalling with [Freebayes](https://github.com/freebayes/freebayes) and [BCFtools](http://samtools.github.io/bcftools/bcftools.html) | ||
| - predicts protein-coding genes for the assemblies using [Prodigal](https://github.com/hyattpd/Prodigal), and bins with [Prokka](https://github.com/tseemann/prokka) and optionally [MetaEuk](https://www.google.com/search?channel=fs&client=ubuntu-sn&q=MetaEuk) | ||
| - performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), and/or with [CONCOCT](https://github.com/BinPro/CONCOCT), and checks the quality of the genome bins using [Busco](https://busco.ezlab.org/), [CheckM](https://ecogenomics.github.io/CheckM/), or [CheckM2](https://github.com/chklovski/CheckM2) and optionally [GUNC](https://grp-bork.embl-community.io/gunc/). | ||
| - performs metagenome binning using [MetaBAT2](https://bitbucket.org/berkeleylab/metabat/src/master/), [MaxBin2](https://sourceforge.net/projects/maxbin2/), [CONCOCT](https://github.com/BinPro/CONCOCT), and/or [COMEBin](https://github.com/ziyewang/COMEBin) |
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Maybe mention optional Comebin here
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They are all optional in one away another so I think this it is necessary in this case :)
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@prototaxites any chance could get the second ✔️ ? For the final conda error I have ZERO clue wtf is going on with conda and genomad... I check the _Note: I do see that the interactive log also says at one point <...>
│ Executing geNomad summary (v1.11.0). This will summarize the results │
<...>
(/home/james/cache/conda/env-465262dfb55483f0-1e2473494fae4e0dcccc5405c7f2e608) james@bionb103:~/git/nf-core/mag/testing/work/19/522486db3a849dae9fd17d72376a39 (dev)$ cat versions.yml
"NFCORE_MAG:MAG:VIRUS_IDENTIFICATION:GENOMAD_ENDTOEND":
genomad: 1.9.4
(/home/james/cache/conda/env-465262dfb55483f0-1e2473494fae4e0dcccc5405c7f2e608) james@bionb103:~/git/nf-core/mag/testing/work/19/522486db3a849dae9fd17d72376a39 (dev)$ conda deactivate
(nf-core) james@bionb103:~/git/nf-core/mag/testing/work/19/522486db3a849dae9fd17d72376a39 (dev)$ less .command.sh
(nf-core) james@bionb103:~/git/nf-core/mag/testing/work/19/522486db3a849dae9fd17d72376a39 (dev)$ less .command.run
(nf-core) james@bionb103:~/git/nf-core/mag/testing/work/19/522486db3a849dae9fd17d72376a39 (dev)$ source $(conda info --json | awk '/conda_prefix/ { gsub(/"|,/, "", $2); print $2 }')/bin/activate /home/james/cache/conda/env-465262dfb55483f0-1e2473494fae4e0dcccc5405c7f2e608
(/home/james/cache/conda/env-465262dfb55483f0-1e2473494fae4e0dcccc5405c7f2e608) james@bionb103:~/git/nf-core/mag/testing/work/19/522486db3a849dae9fd17d72376a39 (dev)$ genomad --version
geNomad, version 1.11.0If I remove all output files and run the command within the environment in the I get As expected 🙃 So I'm inclined to just ignore this one failure for now... |
prototaxites
approved these changes
Oct 26, 2025
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prototaxites
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Yes, looks good from a changes point of view to me!
That conda issue is a bit concerning, though. Do you see the same if you run a local test?
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The string 1.9.4 doesn't even exist in the geNomad repository of that version?!!
Yes, all my examples about are from local tests... And if I load the conda environment in VScode and do a global code search I also cannot find |
dialvarezs
approved these changes
Oct 26, 2025
jfy133
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Oct 26, 2025
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Mostly optimisations or bug fixes - primary new functionality is new binner COMEBIN
Addedlongread_percentidentityandshortread_percentidentityand set the value oflongread_percentidentityin thetest_fullprofile to 85 (by @prototaxites)ChangedTEMPLATE(by @jfy133)FixedDependencies