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Upgrade simpleaf and alevinqc #361
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Thanks for the PR!
I can create another PR for updating the documentation if you think this might be useful!!
That would be fantastic!
@@ -2,10 +2,10 @@ process SIMPLEAF_INDEX { | |||
tag "$transcript_gtf" | |||
label "process_medium" | |||
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conda 'bioconda::simpleaf=0.10.0-1' |
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Would it be possible to switch to the central nf-core/modules
version at this point (see also #296)?
There are modules for simpleaf_index and simpleaf_quant already, they might also need slight updates though.
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The modules look good and switching to that would reduce the maintenance burden of simpleaf for nf-core.
Should I submit a PR there? How should I merge the changes there back to scrnaseq
?
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yes please! Once the module PRs are merged, you can simply install them with the nf-core tools
CLI that you also use for linting:
nf-core modules install
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Cool! Thanks for the information. I will work on this next week! BTW, the other account, an-altosian, is also me :)
The nf-core CLI provides some linting check that ensures certain quality and consistency criteria are met. The same checks are performed by the CI (see "nf-core linting" check below) and is currently failing because of |
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For For nf-core linting / pre-commit (pull_request), I ran |
Let's worry about linting as the last step once you switched to the central nf-core modules. |
Dear scrnaseq developers (and @rob-p, of course ;P ),
This PR is related to #312. I did the following things:
no_piscem
innextflow.config
for switching from the defaultpiscem
mapper to salmonuse_selective_alignment
innextflow.config
for switching the mapping strategy from the default pseudo-alignment with structure constraints to selective alignmentCitation.md
*_t2g_3col.tsv
with*t2g_3col.tsv
inSIMPLEAF_INDEX
process because the latest simpleaf calls itt2g_3col.tsv
, without prefixsalmon_index
parameter withsimpleaf_index
, because the latest simpleaf can take both prebuilt salmon and piscem indices andsalmon_index
seems not precise anymore. Please feel free to change this back.Moreover,
alevin-fry
andsimpleaf,
as standalone software tools, are the successors of thealevin
module insalmon
. In the documentation, I saw thatsalmon
,salmon alevin
,alevin-fry
, andsimpleaf
are used interchangeably. Although it doesn't hurt, it might cause confusion because the output directory generated by them have distinct layouts and contents. It might be great if we could update the doc. I can create another PR for updating the documentation if you think this might be useful!!PR checklist
nf-core lint
).Sorry, I don't know what this means.
nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.As I am not sure when this PR will be merged, I leave it here.
README.md
is updated (including new tool citations and authors/contributors).