Dev -> Master for 3.11 release #966

drpatelh · 2023-03-20T10:44:06Z

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… (Lexogen kits as examples for inline UMIs in R1).

Add further example parameters to the UMI section of the manual.

This proposed section provides parameters for the QuantSeq FWD 3' mRNA sequencing protocol.

BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME was mistakenly written as BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME, causing the workflow to error out in case the UMI option was set when using HISAT2. Fixes #929.

Adding recommended parameters for 3' tag RNA-seq (e.g. QuantSeq) data

Fix typo preventing the use of UMI processing with HISAT2

Cache data for GHA

…rgs in the STAR module.

…nique(false) in contrast returns a new, deduplicated list and leaves the params intact.

Linting with the new version of Black 23.1

…licates Deduplication for the ext.args of the STAR module

github-actions · 2023-03-29T12:10:10Z

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The version already includes the "v" prefix, so no need to add it in the json. I also fixed the name, which was hardcoded to a different workflow.

Tower actions testing

hotfix: Self hosted tests March 23

Remove self-hosted runner definitions in Actions CI

drpatelh · 2023-03-29T21:19:13Z

@nf-core-bot fix linting

MatthiasZepper and others added 30 commits January 10, 2023 18:08

Add further example parameters to the UMI section of the usage manual…

910d98d

… (Lexogen kits as examples for inline UMIs in R1).

Merge pull request #926 from MatthiasZepper/umi_params

36e9206

Add further example parameters to the UMI section of the manual.

Added 3′ digital gene expression assays section

da6233b

This proposed section provides parameters for the QuantSeq FWD 3' mRNA sequencing protocol.

Fix typo preventing the use of UMI processing with HISAT2

fb7117c

BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS_GENOME was mistakenly written as BAM_DEDUP_STATS_SAMTOOLS_UMI_UMITOOLS_GENOME, causing the workflow to error out in case the UMI option was set when using HISAT2. Fixes #929.

Apply suggestions from code review

59cbe73

[automated] Fix linting with Prettier

8000e0c

Merge pull request #928 from tomsing1/master

a5ebd3e

Adding recommended parameters for 3' tag RNA-seq (e.g. QuantSeq) data

Merge pull request #930 from DIncalciLab/fix-umi-typo

c58694e

Fix typo preventing the use of UMI processing with HISAT2

Add tests samplesheet in the main repo

ea237f4

add params.test_data_base

ba19814

this is why you should not edit JSON files

f1941ae

trying to use local files

e2e574a

use samplesheet in the test_data repo

2d8c44c

fix path

0b4b19b

fix path

423ba0b

fix path

785ea73

fix path

f9f467c

uncache data

bd4f148

re-cache data

8770ee6

should not have updated the data that is cached...

1c3dcc1

Merge pull request #933 from maxulysse/cache_test_data

ee0d80f

Cache data for GHA

Linting with the new version of Black 23.1'

6b86d7f

Revert linting for JSON files.

3a833dc

deduplication for the union of ext.args and params.extra_star_align_a…

cbf4dbd

…rgs in the STAR module.

.unique() modifies the original list and nukes all Nextflow params. u…

2586006

…nique(false) in contrast returns a new, deduplicated list and leaves the params intact.

Changelog update with PR.

8051df9

.split() would be invoked on empty string with parameter is unset.

869fab4

Merge pull request #935 from MatthiasZepper/Linting_Black23.1

f52d8e9

Linting with the new version of Black 23.1

Update CHANGELOG.md

595ca66

Merge pull request #934 from MatthiasZepper/extra_star_align_args_dup…

48e683e

…licates Deduplication for the ext.args of the STAR module

Update work directory to match old runners

22db014

robsyme and others added 14 commits March 29, 2023 13:16

Use env for run name

3ee41ab

Remove github.event.pull_request.head.label

29cf6ab

Rely on action to remove colons from branch name

79c354f

Remove double underscore

8fab0d9

Bump actions versions

1a88aa8

Minimize run names to remove tag/branch/commit

7957933

Fix #975

bb41bbc

Replace System.exit(1) calls in pipeline template

baa7aa3

Fix nf-core lint

7b8abfc

Add explicit test_full profiles for all cloud providers

aa407f4

Update nextflow.config

565e970

Update nextflow.config

257fd7e

Update nextflow.config

530c813

Minor fixes for JSON sent to Slack.

fe39f59

The version already includes the "v" prefix, so no need to add it in the json. I also fixed the name, which was hardcoded to a different workflow.

MatthiasZepper mentioned this pull request Mar 29, 2023

Create patches for umi-tools #983

Closed

9 tasks

drpatelh and others added 4 commits March 29, 2023 14:26

Merge pull request #981 from nf-core/tower-actions-testing

5b2b523

Tower actions testing

fix: Switched all tests to run on self-hosted instead of Github hosted

5c676f4

Revert linting to use GHA hosted

232cbf3

Merge pull request #984 from nf-core/self_hosted_tests_march_23

8aab2cc

hotfix: Self hosted tests March 23

MatthiasZepper mentioned this pull request Mar 29, 2023

umi-tools: Choose different process labels nf-core/modules#3219

Merged

14 tasks

drpatelh and others added 3 commits March 29, 2023 14:53

Update CHANGELOG

b4219ef

Update other CI tests

d50a30d

Merge pull request #986 from drpatelh/hosted

c51d105

Remove self-hosted runner definitions in Actions CI

nf-core-bot and others added 3 commits March 29, 2023 22:10

[automated] Fix linting with Prettier

61c6050

Update CHANGELOG.md

0b206d2

Update cloud_tests_full.yml

fbffe86

drpatelh merged commit 48fb9b4 into master Mar 30, 2023

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Dev -> Master for 3.11 release #966

Dev -> Master for 3.11 release #966

drpatelh commented Mar 20, 2023

github-actions bot commented Mar 29, 2023

drpatelh commented Mar 29, 2023

Dev -> Master for 3.11 release #966

Dev -> Master for 3.11 release #966

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drpatelh commented Mar 20, 2023

github-actions bot commented Mar 29, 2023

Python linting (black) is failing

drpatelh commented Mar 29, 2023

Python linting (`black`) is failing