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Merge pull request #269 from nf-core/dev
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@apeltzer
apeltzer authored Oct 7, 2024
2 parents 17cde5d + 774f773 commit ebefeef
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4 changes: 3 additions & 1 deletion .github/workflows/ci.yml
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Expand Up @@ -77,10 +77,12 @@ jobs:
--shard ${{ matrix.shard }}/${{ env.SHARDS }} \
--changed-since HEAD^ \
--profile "+${{ matrix.profile }}" \
--filter pipeline
--filter pipeline \
--junitxml=test.xml
- name: Publish Test Report
uses: mikepenz/action-junit-report@v3
if: always() # always run even if the previous step fails
with:
report_paths: test.xml
annotate_only: true
9 changes: 7 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -3,13 +3,18 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## 1.5.2dev (UNRELEASED)
## 1.5.2 - 2024-10-07

## 1.5.1
### `Changed`

- [#263](https://github.com/nf-core/demultiplex/pull/263) Updated all modules and subworkflows, and added new bclconvert test profile.

## 1.5.1 - 2024-08-20

### `Fixed`

- [#253](https://github.com/nf-core/demultiplex/pull/253) Fixed mkfastq output channels.
- [#265](https://github.com/nf-core/demultiplex/pull/265) Fixed adapter removal for input samplesheets without lane information.

## 1.5.0 - 2024-08-12

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4 changes: 2 additions & 2 deletions assets/multiqc_config.yml
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@@ -1,8 +1,8 @@
report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/demultiplex/releases/tag/1.5.1" target="_blank">nf-core/demultiplex</a>
This report has been generated by the <a href="https://github.com/nf-core/demultiplex/releases/tag/1.5.2" target="_blank">nf-core/demultiplex</a>
analysis pipeline. For information about how to interpret these results, please see the
<a href="https://nf-co.re/demultiplex/1.5.1/docs/output" target="_blank">documentation</a>.
<a href="https://nf-co.re/demultiplex/1.5.2/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-demultiplex-methods-description":
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27 changes: 27 additions & 0 deletions conf/test_bclconvert.config
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@@ -0,0 +1,27 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a fast and simple pipeline test.
Use as follows:
nextflow run nf-core/demultiplex -profile test,<docker/singularity> --outdir <OUTDIR>
----------------------------------------------------------------------------------------
*/

params {
config_profile_name = 'Test bclconvert profile'
config_profile_description = 'Minimal test dataset to check bclconvert pipeline function'

// Limit resources so that this can run on GitHub Actions
max_cpus = 2
max_memory = '6.GB'
max_time = '6.h'

// Input data
input = 'https://huggingface.co/datasets/nf-core/demultiplex/resolve/main/testdata/Miniseq_truseq_smrna/input_samplesheet.csv'
demultiplexer = 'bclconvert'
skip_tools = 'samshee'

}
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36 changes: 18 additions & 18 deletions modules.json
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Expand Up @@ -7,77 +7,77 @@
"nf-core": {
"bases2fastq": {
"branch": "master",
"git_sha": "c651992bf8425fecefe14085ff486f42172cba77",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"bcl2fastq": {
"branch": "master",
"git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["bcl_demultiplex"]
},
"bclconvert": {
"branch": "master",
"git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["bcl_demultiplex"]
},
"cellranger/mkfastq": {
"branch": "master",
"git_sha": "61123e49c6034920eb6f312ad71e4815a7853257",
"git_sha": "a90a8863a3408e15d5a339b06413e57cf9ca9860",
"installed_by": ["modules"]
},
"checkqc": {
"branch": "master",
"git_sha": "337bc962d03c2e08a728c9bf731a2148e323e731",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"falco": {
"branch": "master",
"git_sha": "a236d2c2ec9e68db9b8501105d804acb359552b5",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fastp": {
"branch": "master",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"fqtk": {
"branch": "master",
"git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"kraken2/kraken2": {
"branch": "master",
"git_sha": "a13d5d945742a60bbef6e5c177e81cda540f75dc",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_contam_seqtk_kraken"]
},
"md5sum": {
"branch": "master",
"git_sha": "1164836d4d3922ab937865b17086485f0f472748",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396",
"git_sha": "b8d36829fa84b6e404364abff787e8b07f6d058c",
"installed_by": ["modules"]
},
"seqtk/sample": {
"branch": "master",
"git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["fastq_contam_seqtk_kraken"]
},
"sgdemux": {
"branch": "master",
"git_sha": "574074e6ea2497b53df1f226473a8c71524af0d0",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
},
"untar": {
"branch": "master",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
"installed_by": ["modules"]
}
}
Expand All @@ -86,7 +86,7 @@
"nf-core": {
"bcl_demultiplex": {
"branch": "master",
"git_sha": "22261833fced91665b986c6833e91a4a5cccb0a9",
"git_sha": "a6e6bec1b1da613b89a6c0a3a46713f880cf5aca",
"installed_by": ["subworkflows"]
},
"fastq_contam_seqtk_kraken": {
Expand All @@ -96,12 +96,12 @@
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3",
"git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab",
"installed_by": ["subworkflows"]
},
"utils_nfvalidation_plugin": {
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127 changes: 84 additions & 43 deletions modules/nf-core/bases2fastq/meta.yml
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