avoid mpileup writing to inputdir

[pavanvidem]

FOR CONTRIBUTOR:

• - I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• - License permits unrestricted use (educational + commercial)
• - This PR adds a new tool or tool collection
• - This PR updates an existing tool or tool collection
• - This PR does something else (explain below)

[bgruening]

@pavanvidem your medaka commit is still in here. Can you please clean that.

ping @natefoo

[bgruening]

is the str() needed here?

[wm75]

also, ref.fa doesn't need quoting, but $reference_source.ref_file.fields.path might.

[pavanvidem]

maybe. I just copied it from calmd here

tools-iuc/tool_collections/samtools/samtools_calmd/samtools_calmd.xml

Line 16 in 11249b4

#set ref_fa = str( $reference_source.ref_fasta.fields.path )

[bernt-matthias]

Maybe we should integrate this in #3740 .. and check if other samtools wrappers do the same mistake.

[bernt-matthias]

Ideally the tool should use the @PREPARE_FASTA_IDX@ token? Probably the conditional and maybe in included parameters need to be renamed.

sam_to_bam and calmd could be treated the same way.

[bernt-matthias]

I will merge this into #3740

[wm75]

@bernt-matthias I had assumed the missing version bump was on purpose here to fix the tool silently?
Merging things into the larger samtools update will leave public servers with an executable tool version that misbehaves.

@bgruening @natefoo am I misunderstanding things?

[bernt-matthias]

@wm75 .. I see. Then lets merge, or @bgruening?

[bernt-matthias]

The changes that I have suggested are now implemented in #3740

I also cherry-picked the commit from the PR which should not hurt .. maybe I need to merge after this one is in.

[bgruening]

ping @pavanvidem

[pavanvidem]

I also implemented the suggested changes today morning. I'm pushing my changes now, then I will check if there something that I can adapt from #3740

[bernt-matthias]

I also implemented the suggested changes today morning. I'm pushing my changes now, then I will check if there something that I can adapt from #3740

I would suggest to keep it as is, i.e. pavanvidem@b12876b

Otherwise we might need a version bump and loose the possibility for a "silent update".

[pavanvidem]

The changes shouldn't affect any functionality. Can't we do a silent update here?

[bernt-matthias]

The changes shouldn't affect any functionality. Can't we do a silent update here?

Renaming parameters might affect workflows. So I would say: No

[pavanvidem]

Agree, makes sense.

[bernt-matthias]

Good to go @bgruening and @wm75?

[wm75]

LGTM. Sorry for the back and forth here @pavanvidem

[pavanvidem]

all good @wm75, thank you and @bernt-matthias for the review

[bernt-matthias]

I will merge this if @bgruening does not object..