Release 1.2 #84

muffato · 2023-12-18T13:02:02Z

It's release time !

PR checklist

This comment contains a description of changes (with reason).
If you've fixed a bug or added code that should be tested, add tests!
If you've added a new tool - have you followed the pipeline conventions in the contribution docs
Make sure your code lints (nf-core lint).
Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
Usage Documentation in docs/usage.md is updated.
Output Documentation in docs/output.md is updated.
CHANGELOG.md is updated.
README.md is updated (including new tool citations and authors/contributors).

Syncing main to dev

… `pipeline_info`

Added the cleanup profile and use it for our Tower Sanger tests

New tolsoft details

Add read group back and crumble for HiFi

Closes #81

…SF exit codes

…manipulate

…in the UR field of the @sq headers

Updated the docs before release

Resource optimisation

muffato · 2023-12-18T13:36:16Z

@priyanka-surana : do you remember the version of the nf-core template you last used in this pipeline ?

priyanka-surana · 2023-12-18T14:08:18Z

@priyanka-surana : do you remember the version of the nf-core template you last used in this pipeline ?

Based on the dates, my best guess is v2.9.

muffato · 2023-12-18T14:35:37Z

I'm getting a few nf-core lint --release failures:

╭─ [✗] 6 Pipeline Tests Failed ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                        │
│ nextflow_config: Config variable not found: params.validationShowHiddenParams                                                                                                          │
│ nextflow_config: Config variable not found: params.validationSchemaIgnoreParams                                                                                                        │
│ files_unchanged: .github/PULL_REQUEST_TEMPLATE.md does not match the template                                                                                                          │
│ files_unchanged: .github/workflows/branch.yml does not match the template                                                                                                              │
│ files_unchanged: .github/workflows/linting.yml does not match the template                                                                                                             │
│ schema_params: Param schema_ignore_params from nextflow config not found in nextflow_schema.json                                                                                       │
│                                                                                                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

I'm looking into those.

priyanka-surana · 2023-12-18T14:43:52Z

I'm getting a few nf-core lint --release failures:

╭─ [✗] 6 Pipeline Tests Failed ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│                                                                                                                                                                                        │
│ nextflow_config: Config variable not found: params.validationShowHiddenParams                                                                                                          │
│ nextflow_config: Config variable not found: params.validationSchemaIgnoreParams                                                                                                        │
│ files_unchanged: .github/PULL_REQUEST_TEMPLATE.md does not match the template                                                                                                          │
│ files_unchanged: .github/workflows/branch.yml does not match the template                                                                                                              │
│ files_unchanged: .github/workflows/linting.yml does not match the template                                                                                                             │
│ schema_params: Param schema_ignore_params from nextflow config not found in nextflow_schema.json                                                                                       │
│                                                                                                                                                                                        │
╰────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯

I think it is a nf-core version mismatch.

muffato · 2023-12-18T15:12:53Z

You were right ! No issue reported with nf-core 2.7

muffato · 2023-12-18T15:13:42Z

In that case, the PR is now ready for review

priyanka-surana

Since all the changes were reviewed in dev, I think we are good to merge.

We're so good. We're professionals. We're the best. ToL-IT power !

priyanka-surana and others added 30 commits March 16, 2023 19:20

Merge pull request #61 from sanger-tol/main

cf7b3e0

Syncing main to dev

add read group tag back

c369d10

add crumble for pacbio hifi

fd15eae

update merge args

45d4dec

update bed output name

0995917

update crumble outdir name

a2a3751

modules update

188e708

prettier fix

76e3c41

Added the cleanup profile and use it for our Tower Sanger tests

ff6fb57

Latest nomenclature

7fa1b83

Use the latest version of the Tower action

4b89961

Our latest convention is to use one directory per pipeline, all under…

0491dcc

… `pipeline_info`

Update sanger_test.yml

a89dfee

Update sanger_test_full.yml

1c724f6

Update sanger_test.yml

ab21cb1

Update sanger_test_full.yml

bc90069

Merge pull request #79 from sanger-tol/cleanup_ci

35119f4

Added the cleanup profile and use it for our Tower Sanger tests

New tolsoft details

4d7bc41

Fixed the repository name

aebfb83

Merge pull request #80 from sanger-tol/new_tolsoft_details

093b313

New tolsoft details

Merge pull request #68 from sanger-tol/crumble

0262a3f

Add read group back and crumble for HiFi

Collect the read counts from the input files

2109bed

Collect the size of the genome (file size is a good proxy)

e2e8ead

Simply use the whole base name to name the channel

11678fc

Deal with genomes > 4 Gbp

84caa10

Closes #81

Update the read count for SAMTOOLS_MERGE

8dca0f3

Some values are large and need 64 bits

8c67daf

Wrong information

e432d89

Updated the error codes to the latest template versions. Covers all L…

ae6942b

…SF exit codes

Estimate the resource requirements based on the size of the inputs

46e9910

muffato and others added 16 commits December 7, 2023 15:22

Updated the settings for SORMADUP

9da9f3f

Updated the BWA_MEM memory requirement

5e15589

Increased the number of retries

bdbcbb4

The default memory settings work just fine and make things easier to …

3905219

…manipulate

Usage is very close to the trend line. Smaller bins work fine

c15d923

quay.io/ is now the default

4094724

Added optimised settings for crumble

3ef0477

Need to fake REF_PATH to force crumble to use the Fasta file defined …

f0c1ba4

…in the UR field of the @sq headers

There is a difference for ONT, which I assume would be there for CLR too

79bcbbc

Updated the docs before release

63dfaff

add release name

dda2c2e

original version of the png file

01748ac

Forgot to mention --use_work_dir_as_temp

c8e5125

Rename readmapping v3.pptx to readmapping_v3.pptx

d3a84da

Rename readmapping v2.pptx to readmapping_v2.pptx

c522d3d

Merge pull request #83 from sanger-tol/doc

bd02f75

Updated the docs before release

muffato added this to the 1.2.0 milestone Dec 18, 2023

muffato requested a review from priyanka-surana December 18, 2023 13:02

muffato self-assigned this Dec 18, 2023

Merge pull request #82 from sanger-tol/resource_optimisation

0f4e2a1

Resource optimisation

muffato marked this pull request as ready for review December 18, 2023 15:13

priyanka-surana approved these changes Dec 18, 2023

View reviewed changes

We're doing it a day early

db5c8b9

We're so good. We're professionals. We're the best. ToL-IT power !

muffato merged commit 91efc18 into main Dec 19, 2023
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Release 1.2 #84

Release 1.2 #84

muffato commented Dec 18, 2023 •

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muffato commented Dec 18, 2023

priyanka-surana commented Dec 18, 2023

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Release 1.2 #84

Release 1.2 #84

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muffato commented Dec 18, 2023 • edited Loading

PR checklist

muffato commented Dec 18, 2023

priyanka-surana commented Dec 18, 2023

muffato commented Dec 18, 2023

priyanka-surana commented Dec 18, 2023

muffato commented Dec 18, 2023

muffato commented Dec 18, 2023

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muffato commented Dec 18, 2023 •

edited

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