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Bump version to v1.5 #152

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merged 4 commits into from
Apr 9, 2020
Merged

Bump version to v1.5 #152

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51c7834
Bump version to v1.5
ewels Apr 7, 2020
a836c15
Merge branch 'dev' into version-1.5
ewels Apr 9, 2020
f99bf65
Change to rebuild CI
ewels Apr 9, 2020
0ffdf85
Tweak CI commands
ewels Apr 9, 2020
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11 changes: 5 additions & 6 deletions .github/workflows/ci.yml
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Expand Up @@ -16,11 +16,11 @@ jobs:
aligner: ['bismark', 'bismark_hisat', 'bwameth']
include:
- aligner: 'bismark'
options: --bismark_index ${GITHUB_WORKSPACE}/results/reference_genome/BismarkIndex/
ref_index: --bismark_index results/reference_genome/BismarkIndex/
- aligner: 'bismark_hisat'
options: --bismark_index ${GITHUB_WORKSPACE}/results/reference_genome/BismarkIndex/
ref_index: --bismark_index results/reference_genome/BismarkIndex/
- aligner: 'bwameth'
options: --bwa_meth_index ${GITHUB_WORKSPACE}/results/reference_genome/genome.fa
ref_index: --bwa_meth_index results/reference_genome/genome.fa
steps:
- uses: actions/checkout@v2
- name: Install Nextflow
Expand All @@ -30,10 +30,9 @@ jobs:
- name: Pull docker image
run: |
docker pull nfcore/methylseq:dev
docker tag nfcore/methylseq:dev nfcore/methylseq:1.4.1
docker tag nfcore/methylseq:dev nfcore/methylseq:1.5
- name: Run pipeline with test data
run: |
nextflow run ${GITHUB_WORKSPACE} -profile test,docker
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --save_reference
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.options}}
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} ${{matrix.ref_index}}
nextflow run ${GITHUB_WORKSPACE} -profile test,docker --aligner ${{matrix.aligner}} --skip_trimming --rrbs
4 changes: 2 additions & 2 deletions CHANGELOG.md
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@@ -1,6 +1,6 @@
# nf-core/methylseq

## [v1.4.1](https://github.com/nf-core/methylseq/releases/tag/1.4.1) - 2020-04-08
## [v1.5](https://github.com/nf-core/methylseq/releases/tag/1.5) - 2020-04-09

### New features

Expand All @@ -11,7 +11,7 @@

### Software updates

* _new dependency_: pigz `2.3.4`
* _New_: pigz `2.3.4`
* Python base `2.7` > `3.7.3`
* FastQC `0.11.8` > `0.11.9`
* TrimGalore! `0.6.4` > `0.6.5`
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4 changes: 2 additions & 2 deletions Dockerfile
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Expand Up @@ -7,7 +7,7 @@ COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a

# Add conda installation dir to PATH (instead of doing 'conda activate')
ENV PATH /opt/conda/envs/nf-core-methylseq-1.4.1/bin:$PATH
ENV PATH /opt/conda/envs/nf-core-methylseq-1.5/bin:$PATH

# Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-methylseq-1.4.1 > nf-core-methylseq-1.4.1.yml
RUN conda env export --name nf-core-methylseq-1.5 > nf-core-methylseq-1.5.yml
2 changes: 1 addition & 1 deletion environment.yml
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@@ -1,6 +1,6 @@
# You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml
name: nf-core-methylseq-1.4.1
name: nf-core-methylseq-1.5
channels:
- conda-forge
- bioconda
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4 changes: 2 additions & 2 deletions nextflow.config
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Expand Up @@ -80,7 +80,7 @@ params {

// Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev
process.container = 'nfcore/methylseq:1.4.1'
process.container = 'nfcore/methylseq:1.5'

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
Expand Down Expand Up @@ -148,7 +148,7 @@ manifest {
description = 'Methylation (Bisulfite-Sequencing) Best Practice analysis pipeline, part of the nf-core community.'
mainScript = 'main.nf'
nextflowVersion = '>=19.10.0'
version = '1.4.1'
version = '1.5'
}

// Function to ensure that resource requirements don't go beyond
Expand Down