Updating tools/bwameth from version 0.2.6 to 0.2.7

[planemo-autoupdate]

Hello! This is an automated update of the following tool: tools/bwameth. I created this PR because I think the tool's main dependency is out of date, i.e. there is a newer version available through conda.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/bwameth from version 0.2.6 to 0.2.7.

Project home page: https://github.com/brentp/bwa-meth/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.

[bernt-matthias]

Please undo this change and maybe add the explanation from here

tools-iuc/tools/hisat2/hisat2.xml

Line 341 in 3e7bf5a

## Convert SAM output to sorted BAM

Maybe use exactly the command line from over there:

| samtools sort --no-PG -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o output.bam

[bgruening]

I did, but now I have sort: unrecognized option '--no-PG'

[bernt-matthias]

I did, but now I have sort: unrecognized option '--no-PG'

Might bwameth come with a very old samtools version?

Anyway, maybe we should remove it anyway, we recently came to the conclusion that we should not use it: #5985 (comment)

[bernt-matthias]

Can we easily find out which samtools verison is used here? bioconda seems to have no pinning on samtools. I would expect something recent .. seems fishy.

[bgruening]

(planemo) bag@bag:~/projects/code/tools-iuc/tools/jbrowse2$ docker run -i -t --rm quay.io/biocontainers/bwameth:0.2.7--pyh7cba7a3_0 bash
root@3b599841503d:/# samtools --version
samtools 1.6
Using htslib 1.6
Copyright (C) 2017 Genome Research Ltd.

[bernt-matthias]

If you like we can proceed.

samtools 1.6 is 7 years old (container only 1 year) if we want something newer we could bump the container, but this would delay things here.

Up to you :)

[bgruening]

I tried, but realisticially will not have time to work on this "tab" in the next month.