Add support for CheckM as alternative to BUSCO #350

jfy133 · 2022-11-04T08:37:44Z

Note this does not include the integration with the bin_summary reports etc., I will need somone else to contribute that as it reuqires python script updates (which I'm not really comfortble with)

Closes #326

PR checklist

…-sample rather than per-contig)

github-actions · 2022-11-04T08:37:54Z

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CHANGELOG.md

github-actions · 2022-11-04T08:39:18Z

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nf-core/tools version 2.7.2
Run at 2023-01-17 08:50:21

docs/usage.md

skrakau · 2022-11-18T16:14:01Z

CHANGELOG.md

@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Changed`

 - [#340](https://github.com/nf-core/mag/pull/340) - Update to nf-core 2.6.1 `TEMPLATE`
+- [#350](https://github.com/nf-core/mag/pull/350) - Adds support for CheckM as alternative bin completeness and QC tool (added by @jfy133).


Is there a new convention how to state individual contributions? One could also think about changing the contributions section in the README...

Not exactly, but if you tag people in the README, on release they get shown as contributors to that specific release which is a nice acknowledgment of the specific work they do (rather than just the general 'catch all' on the README. I did this on the last 2 MAG releases too:

https://github.com/nf-core/mag/releases/tag/2.2.1
https://github.com/nf-core/mag/releases/tag/2.2.0

But I'm happy to remove it if you don' tlike it.

I see, I just thought it would make sense to do this consistently

Can also do that! Tell me which way you prefer and I'll update accordingly :)

Did you do this in other pipelines as well? I don't mind, we can keep it like this

OK, I don't mind either way. I'll suggest then mention each person for each PR in the CHANGELOG (then it makes it easier to just paste the changelog straight into the release notes and it'll already be there, rather than us having to go back and check each PR afterwards), but ultimately this is your pipeline so you can choose ;)

Hi, I was thinking again about this issue and if I should add my name now or not, and in the end I would somehow prefer not to start this (at least as long it's not nf-core wide like this), because then everyone who is not doing this would be excluded.

OK, well actually in a later PR (from yday), I've gone back through all the merged PRs for the upcoming release and I've added everyone:

#350

So we won't have missed anyone now. Note that these tags only reflect what is displayed in each release (not the contribtuors thorughout the entire project as a whole, which is still displayed here).

Things such as this are not necessary to be nf-core wide to be fair. But as this displaying of the contributors in the release stuff is pretty new anyway, I was sort of thinking maybe nf-core/mag could be the 'forerunner' of a nice practise ;).

But if you prefer, I could also do a poll on slack to ask if people think we should do it nf-core wide or not?

I sort of like it because it again makes it much more visible peoples contributors, and will help encourage people to keep contributing in the long run. But it's up to you! I can also remove all the tags from PR #350 again if you prefer.

Ah, you mean #380, sorry didn't see it.

A poll would be nice though, then we could see how to do it consistently. Even if it doesn't necessarily has to be consistent, it just easier to stick to a certain way across multiple pipelines.
So don't remove it for now.

Oops yes, typo.

Poll here: https://nfcore.slack.com/archives/C043UU89KKQ/p1673621984306899

skrakau · 2022-11-18T16:18:25Z

I will have a more thorough look here and also look at the python scripts asap :)

docs/output.md

skrakau · 2022-11-30T14:36:45Z

Hi @jfy133 and @d4straub, do you have any opinion about which of the checkm metrics should end up in the bin_summary?
e.g. Bin Id Marker lineage # genomes # markers # marker sets Completeness Contamination Strain heterogeneity or more?

Ok, maybe the question is more: the output of checkm lineage_wf or checkm qa?

Edit: will just use all checkm qa results, if you don't object

docs/output.md

jfy133 · 2022-11-30T15:07:21Z

@alexhbnr and @maxibor might also have thoughts on this

jfy133 · 2022-11-30T15:07:47Z

But I believe Alex only actually uses output of qa

alexhbnr · 2022-11-30T15:20:40Z

Yes, I usually first run the wf command to get the output and use the qa command with the additional parameters -o 2 --tab_table to get a nicely formatted TSV table. The latter is required to merge the output with the tool GUNC, which provides yet another approach to estimate the contamination of a MAG.

d4straub · 2022-11-30T15:29:21Z

I actually have no preference for CheckM, because I am not used to it. Usually the more the merrier ;)

jfy133 · 2022-12-01T08:28:30Z

@alexhbnr what are your preferred columns?

alexhbnr · 2022-12-01T12:14:28Z

Here is the list that I usually would have a look at:

Marker lineage
Completeness
Contamination
Strain heterogeneity
Genome size (bp)
"# contigs"
N50 (contigs)
GC
Coding density

…mary.tsv

skrakau · 2022-12-02T11:45:42Z

I added a checkm_summary.tsv file including all bins, as for BUSCO and QUAST
add using the CheckM results also for the filtering step prior running GTDB-Tk
and included the CheckM QA results into bin_summary.tsv (currently all columns)

@jfy133 maybe you can have a look if this seems alright to you.

However, the bin_summary.tsv needs to be adjusted. So far the original column names are used, but QUAST and CheckM generate redundant results, with overlapping column names (e.g. "# contigs", -> becomes "# contigs_x", "# contigs_y"). Also this might get quite confusing if there are multiple N50* columns from different tools, but maybe one can expect that the user knows the exact column names from the different tools. Any preferences how to handle this?

jfy133 · 2022-12-02T20:16:30Z

Table looks OK to me based on my minimal experience (I'll attach an example below, @alexhbnr , looks OK to you?)
bin_summary.tsv: I think keeping just QUAST would be most reliable. It would then give you consistent results regardless of the QC tool; and if you wanted to compare you can always look specifically at CheckM (/BUSCO, even if it doesn't produce that info) results. I don't think it makes sense to add loads of extra redundant columns as it makes it harder to evaluate.

checkm_summary.zip

github-actions · 2022-12-19T16:13:29Z

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skrakau · 2023-01-13T11:39:35Z

maybe worth mentioning: the CheckM results "Bin Id" does not contain a ".fa" extension and I didn't change it, while for the other tools and summaries the name for the bin does contain it.

modules/nf-core/checkm/lineagewf/main.nf

skrakau · 2023-01-13T12:36:56Z

docs/usage.md

+It is _highly_ recommended to pass utilise the `--checkm_db` flag to pass pre-downloaded and uncompressed directory of required CheckM references.
+
+If you do not use this, this will result in the tool detecting the database is missing, and download the files for EVERY CheckM process that is executed.


This should not be the case anymore, right?

nextflow_schema.json

jfy133 · 2023-01-13T14:55:12Z

ts "Bin Id" does not contain a ".fa" extension and I didn't change it, while for the other tools and summaries the name for the bin does contain it.

Do you mean inside the output table?

Otherwise I should have adressed all your other comments @skrakau :)

jfy133 · 2023-01-13T15:10:09Z

Ok for some reason the Black python linting error is now coming up even though I didn't touch that ... when I black locally nothing changes... could you try running it and see if it fixes it for you @skrakau ?

skrakau · 2023-01-17T07:58:55Z

ts "Bin Id" does not contain a ".fa" extension and I didn't change it, while for the other tools and summaries the name for the bin does contain it.

Do you mean inside the output table?

Yes

skrakau

LGTM :)

jfy133 added 6 commits October 7, 2022 15:48

Start CHECKM subworkflow

aa36a0e

Merge remote-tracking branch 'origin/dev' into checkm

ee05d9f

Start work on adding CheckM,

584dd60

TODOs for final stps

a35eb4d

More documentation (missing output and currently trying to run on per…

f23333e

…-sample rather than per-contig)

Fix prefix, staging

68cf671

jfy133 changed the base branch from master to dev November 4, 2022 08:37

jfy133 commented Nov 4, 2022

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Merge branch 'checkm' of github.com:nf-core/mag into checkm

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Update workflow

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Fix CI test

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Generate checkm_summary.tsv, use for GTDB-TK and include into bin_sum…

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…mary.tsv

Add CheckM autodownload iwth patched Aria2 module

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jfy133 and others added 4 commits December 2, 2022 21:18

Add auto-downloading of CheckM data when not supplied by user

73d6b93

Merge branch 'dev' into checkm

e001aaa

Fix handling of checkm results for gtdbtk

9cdf461

Use only subset of checkm results for final bin_summary

954b0c1

jfy133 added 2 commits January 12, 2023 15:54

Merge branch 'dev' into checkm

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Merge branch 'checkm' of github.com:nf-core/mag into checkm

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Merge branch 'dev' into checkm

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Update CHANGELOG

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jfy133 mentioned this pull request Feb 27, 2023

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Add support for CheckM as alternative to BUSCO #350

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		It is _highly_ recommended to pass utilise the `--checkm_db` flag to pass pre-downloaded and uncompressed directory of required CheckM references.

		If you do not use this, this will result in the tool detecting the database is missing, and download the files for EVERY CheckM process that is executed.

Add support for CheckM as alternative to BUSCO #350

Add support for CheckM as alternative to BUSCO #350

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