added ANI filter, vignettes, pathogens to list, fixed a few bugs, tuned fontsize for heatmaps

[LeandroRitter]

No description provided.

[LeandroRitter]

This PR addresses a number of issues, for example #121, #124, #127, #128, #132, #133

[percyfal]

@LeandroRitter only minor comments, LGTM.

[ZoePochon]

There is a small typo that comes up twice in the readme as well : KarkenUniq abundance matrix Instead of KrakenUniq Le mer. 9 août 2023, 16:58, Nikolay Oskolkov ***@***.***> a écrit :

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***@***.**** commented on this pull request. ------------------------------ In workflow/rules/authentic.smk <#134 (comment)>: > @@ -89,7 +92,7 @@ checkpoint Malt_Extract: message: "Malt_Extract: RUNNING MALT EXTRACT FOR SAMPLE {input.rma6}" shell: - "time MaltExtract -i {input.rma6} -f def_anc -o {params.extract} --reads --threads {threads} --matches --minPI 85.0 --maxReadLength 0 --minComp 0.0 --meganSummary -t {input.node_list} -v 2> {log}" + "time MaltExtract -Xmx32G -i {input.rma6} -f def_anc -o {params.extract} -r {params.ncbi_db} --reads --threads {threads} --matches --minPI 85.0 --maxReadLength 0 --minComp 0.0 --meganSummary -t {input.node_list} -v 2> {log}" I believe, the -r flag should be there by default because we have a rule NCBIMapTre that downloads ncbi.map and ncbi.tre and places them to ncbi_db. In case, the downloading fails, when there is not internet connection as TJ noticed, there should be at least a chance to point MaltExtract to ncbi_db where one could manually upload the ncbi.map and ncbi.tre files. I ran aMeta with the -r flag a few times on my laptop and Uppmax, i.e. with internet connection, and it always worked — Reply to this email directly, view it on GitHub <#134 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ASTPL5FRDYBT43EIESXW3ITXUOQPVANCNFSM6AAAAAA234DLI4> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>