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feat: Salmon update #482
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feat: Salmon update #482
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fgvieira
reviewed
Apr 30, 2022
fgvieira
reviewed
Apr 30, 2022
fgvieira
reviewed
Apr 30, 2022
Hi, I solve new errors and come back here asap |
fgvieira
reviewed
May 4, 2022
fgvieira
approved these changes
May 5, 2022
fgvieira
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May 6, 2022
fgvieira
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May 13, 2022
fgvieira
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May 23, 2022
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Description
This PR brings an update of Salmon to 1.8
Decoys, pseudo-bams and gene-map files are handled,
resources
:tempdir
is used to set temporary directory in salmon index. Dedicated errors are raised in salmon quant as well as deprecation warning.Main behavior is changed in salmon index, causing a change break, since multiple input are possible now. Salmon quant interface is not changed and the update should be silent, as long as indexes are re-built by users.
You may notice the test dataset in salmon quant has changed: this is due to the new indexing method used after salmon 1.XXX. It required for unit-testing.
Also, manual decompression is not needed anymore.
QC
For all wrappers added by this PR, I made sure that
input:
andoutput:
file paths in the resulting rule can be changed arbitrarily,threads: x
statement withx
being a reasonable default,map_reads
for a step that maps reads),environment.yaml
specifications follow the respective best practices,input:
oroutput:
),Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.),stderr
and/orstdout
are logged correctly (log:
), depending on the wrapped tool,tempfile.gettempdir()
points to (see here; this also means that using any Pythontempfile
default behavior works),meta.yaml
contains a link to the documentation of the respective tool or command,Snakefile
s pass the linting (snakemake --lint
),Snakefile
s are formatted with snakefmt,