Fix cellranger and bump version to 2.5.1 #288

grst · 2024-01-18T11:48:12Z

Somehow the cellranger module installed from modules was missing files, don't ask me how we ended up
there
params.aligner was referenced incorrectly in scrnaseq.nf
Bump version to 2.5.1 to make a patch release

PR checklist

github-actions · 2024-01-18T11:49:44Z

`nf-core lint` overall result: Passed ✅ ⚠️

Posted for pipeline commit 0a674f5

+| ✅ 161 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

nextflow_config - Config manifest.version should end in dev: 2.5.1

❔ Tests ignored:

files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
template_strings - template_strings

✅ Tests passed:

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readme - README Nextflow minimum version badge matched config. Badge: 23.04.0, Config: 23.04.0
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schema_lint - Schema lint passed
schema_lint - Schema title + description lint passed
schema_lint - Input mimetype lint passed: 'text/csv'
schema_params - Schema matched params returned from nextflow config
system_exit - No System.exit calls found
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Run details

nf-core/tools version 2.11.1
Run at 2024-01-22 07:25:06

grst · 2024-01-19T06:58:46Z

@nf-core-bot please fix linting

grst · 2024-01-19T07:00:24Z

@nf-core-bot fix linting

grst · 2024-01-19T07:01:27Z

Don't be nice to the bot -.-

* Somehow the cellranger module was incomplete, don't ask me how we ended up there * params.aligner was referenced incorrectly in scrnaseq.nf

grst · 2024-01-19T07:06:48Z

@nf-core-bot fix linting

fmalmeida

Looks good.
Most of the changes were automatically via nf-core update right?

fmalmeida · 2024-01-22T10:21:01Z

.github/workflows/ci.yml

            "test,docker --aligner alevin",
            "test,docker --aligner kallisto",
            "test,docker --aligner star",
-            "test,docker --aligner cellranger -stub",
-            "test,docker --aligner universc -stub",
+            "test,docker --aligner cellranger",


What was the thing that was making it being - stub before?

grst · 2024-01-22T10:26:34Z

yes... the only two "real" changes are the params.aligner fix and the changes to ci.yml

vondoRishi · 2024-04-04T07:42:15Z

I have run into error with test while running with test profile

nextflow run \
    nf-core/scrnaseq \
    --outdir test_out \
    -r 2.5.1 \
    -profile test

The error is

Command error:
.command.sh: line 2: samtools: command not found

Next, I have tried to test run with cellranger

nextflow run \
    nf-core/scrnaseq \
    --outdir test_out \
    --aligner cellranger \
    -r 2.5.1 \
    -profile test

This time the error is

Command error:
.command.sh: line 3: cellranger: command not found

fmalmeida · 2024-04-04T07:43:47Z

Hello hello,
You have also to select an execution profile.
Maybe,
-profile docker,test.

vondoRishi · 2024-04-04T08:27:51Z

Hello hello, You have also to select an execution profile. Maybe, -profile docker,test.

My silly mistake.
One more thing, the parameter --genome_fasta in the usage example is no longer exist. It should be only --fasta.
Thanks a lot.

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grst changed the base branch from master to dev January 18, 2024 11:48

grst added 7 commits January 19, 2024 08:04

Update modules and fix missing variable error

8df7a8e

* Somehow the cellranger module was incomplete, don't ask me how we ended up there * params.aligner was referenced incorrectly in scrnaseq.nf

trigger ci

91c479a

format with black

f15e8e5

Temporarily disable universc CI

d56741d

Exclude CI For cellrangerarc and universc

1c1592d

Refer to issue numbers for missing test

505d221

Update changelog

46dd143

grst force-pushed the module-update branch from f85ebee to 46dd143 Compare January 19, 2024 07:06

nf-core-bot and others added 2 commits January 19, 2024 07:07

[automated] Fix linting with Prettier

5e428c3

bump version to 2.5.1

621f7cd

grst changed the title ~~Update modules and fix missing variable error~~ Fix cellranger and bump version to 2.5.1 Jan 22, 2024

Merge remote-tracking branch 'origin/dev' into module-update

0a674f5

grst requested a review from fmalmeida January 22, 2024 10:18

fmalmeida approved these changes Jan 22, 2024

View reviewed changes

grst merged commit 737ef17 into dev Jan 22, 2024
12 checks passed

grst deleted the module-update branch January 22, 2024 10:30

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Fix cellranger and bump version to 2.5.1 #288

Fix cellranger and bump version to 2.5.1 #288

grst commented Jan 18, 2024 •

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❗ Test warnings:

❔ Tests ignored:

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grst commented Jan 19, 2024

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vondoRishi commented Apr 4, 2024

fmalmeida commented Apr 4, 2024

vondoRishi commented Apr 4, 2024

Fix cellranger and bump version to 2.5.1 #288

Fix cellranger and bump version to 2.5.1 #288

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nf-core lint overall result: Passed ✅ ⚠️

❗ Test warnings:

❔ Tests ignored:

✅ Tests passed:

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grst commented Jan 19, 2024

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`nf-core lint` overall result: Passed ✅ ⚠️