Updating tools/varvamp from version 1.2.0 to 1.2.1

[gxydevbot]

Hello! This is an automated update of the following tool: tools/varvamp. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.

I have updated tools/varvamp from version 1.2.0 to 1.2.1.

Project home page: https://github.com/jonas-fuchs/varVAMP/releases

For any comments, queries or criticism about the bot, not related to the tool being updated in this PR, please create an issue here.

If you want to skip this change, close this PR without deleting the branch. It will be reopened if another change is detected.

Any commit from another author than 'planemo-autoupdate' will prevent more auto-updates.

To ignore manual changes and allow autoupdates, delete the branch.

[gxydevbot]

There are new updates, they have been integrated to the PR, check the file diff.

[bgruening]

@jonas-fuchs, you changed the FASTA header line to include varVAMP- and dropped more specific information instead. Was this intended?

[jonas-fuchs]

@bgruening Which info do you mean? I mainly changed the bed file format to be artic compatible and included that you can name your scheme. Indeed some information is lost in the main outputs, but e.g. the primer names and penalties you still have this info in the tsv and primer all files.

[bgruening]

Test are failing here for example because of that diff

Output ambiguous_consensus:  different than expected, difference (using diff):
( /tmp/tmp2ak5l8smambiguous_consensus.fasta v. /tmp/tmpgu9586ieambiguous_consensus.fasta )
--- local_file
+++ history_data
@@ -1,2 +1,2 @@
->ambiguous_consensus
+>varVAMP_consensus
 tatcccgtrtycaractgayatccttattaayytgatgcaaccycgrcagcttgtkttccgrccygaagtyytstggaaycayccgatccagcgrgtyatacataatgagctggagcartactgccgwgcycgygctggycgytgyctkgargtkggsgcycayccaagatcyatyaatgayaacccyaatgtyytgcaccggtgcttyctycgcccggtyggdagagaygtmcagcgytggtaytcygccccsacycgyggyccagcggcyaaytgccgccgytcygcgctacgyggyytgccccctgtcgaycgyacmtaytgcttcgacgggttytcccgctgcgcytttgccgctgagacyggratygctttataytcactrcatgacctytggccytcggaygtygcggaggcya

[jonas-fuchs]

Renaming of the fasta header was intended. The name of the file hasn t changed giving the info which consensus it is. Sry about the trouble 😅

[bgruening]

this was a warning before

[wm75]

sorry, what was the warning? Cannot find it.

[wm75]

everything else looks easy enough to fix :-)

[bgruening]

That -n is deprecated and I should use the long version

[gxydevbot]

There are new updates, if you want to integrate them, close the PR and delete branch.

[wm75]

handled in #6486