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drpatelh merged 16 commits into from
Jan 27, 2020
Merged

Fix a couple of things in CHANGELOG #483

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05aedd5
Update CHANGELOG
drpatelh Jan 24, 2020
2302351
Merge branch 'dev' of https://github.com/nf-core/tools
drpatelh Jan 24, 2020
509812a
Rewording
drpatelh Jan 24, 2020
8c6d27f
Update wording
drpatelh Jan 24, 2020
0528876
Fix tag
drpatelh Jan 24, 2020
c16e283
Update version
drpatelh Jan 24, 2020
ad243f3
Update wording
drpatelh Jan 24, 2020
d7456c5
Remove CircleCI everywhere
drpatelh Jan 24, 2020
d1051be
Add README path to igenomes.config
drpatelh Jan 26, 2020
952f8fd
Update CHANGELOG
drpatelh Jan 26, 2020
4c15bcf
Fix merge conflicts
drpatelh Jan 27, 2020
95f0321
Update CHANGELOG
drpatelh Jan 27, 2020
d4995b8
Travis CI definitely going out the door
drpatelh Jan 27, 2020
0815ee0
Update path to transferred issue
drpatelh Jan 27, 2020
07c46f2
Merge branch 'dev' of https://github.com/nf-core/tools
drpatelh Jan 27, 2020
493ca1e
Update CHANGELOG agaaaaaain
drpatelh Jan 27, 2020
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26 changes: 17 additions & 9 deletions CHANGELOG.md
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Expand Up @@ -2,6 +2,13 @@

## v1.8

### Continuous integration

* GitHub Actions CI workflows are now included in the template pipeline
* Please update these files to match the existing tests that you have in `.travis.yml`
* Travis CI tests will be deprecated from the next `tools` release
* Linting will generate a warning if GitHub Actions workflows do not exist and if applicable to remove Travis CI workflow file i.e. `.travis.yml`.

### Tools helper code

* Refactored the template synchronisation code to be part of the main nf-core tool
Expand All @@ -15,20 +22,20 @@
### Linting

* Adjusted linting to enable `patch` branches from being tested
* Warn if GitHub actions workflows do not exist, warn if `.travis.yml` and circleCI are there
* Lint for `Singularity` file [and remove it](https://github.com/nf-core/tools/issues/458)
* Added linting of GitHub actions workflows `linting.yml`, `ci.yml` and `branch.yml`
* Warn if GitHub Actions workflows do not exist, warn if `.travis.yml` and circleCI are there
* Lint for `Singularity` file and raise error if found [#458](https://github.com/nf-core/tools/issues/458)
* Added linting of GitHub Actions workflows `linting.yml`, `ci.yml` and `branch.yml`
* Warn if pipeline name contains upper case letters or non alphabetical characters [#85](https://github.com/nf-core/tools/issues/85)
* Make CI tests of lint code pass for releases

### Template pipeline

* Fixed incorrect paths in iGenomes config as described in issue [#418](https://github.com/nf-core/tools/issues/418)
* Fixed [incorrect usage of non-existant parameter](https://github.com/nf-core/tools/issues/446) in the template
* Fixed incorrect usage of non-existent parameter in the template [#446](https://github.com/nf-core/tools/issues/446)
* Add UCSC genomes to `igenomes.config` and add paths to all genome indices
* Change `maxMultiqcEmailFileSize` parameter to `max_multiqc_email_size`
* Export conda environment in Docker file [#349](https://github.com/nf-core/tools/issues/349)
* Change remaining parameters from `camelCase` to `snakeCase` [#39](https://github.com/nf-core/hic/issues/39)
* Change remaining parameters from `camelCase` to `snake_case` [#39](https://github.com/nf-core/hic/issues/39)
* `--singleEnd` to `--single_end`
* `--igenomesIgnore` to `--igenomes_ignore`
* Having the old camelCase versions of these will now throw an error
Expand All @@ -42,12 +49,13 @@
* Add link to [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) and [Semantic Versioning](http://semver.org/spec/v2.0.0.html) to CHANGELOG
* Adjusted `.travis.yml` checks to allow for `patch` branches to be tested
* Add Python 3.7 dependency to the `environment.yml` file
* Remove awsbatch profile cf [nf-core/configs#71](https://github.com/nf-core/configs/pull/71)
* Remove `awsbatch` profile cf [nf-core/configs#71](https://github.com/nf-core/configs/pull/71)
* Make `scrape_software_versions.py` compatible with Python3 to enable miniconda3 in [base image PR](https://github.com/nf-core/tools/pull/462)
* Add GitHub actions workflows and respective linting
* Add NXF_ANSI_LOG as global environment variable to template GitHub actions CI workflow
* Fixed global environment variable in GitHub actions CI workflow
* Add GitHub Actions workflows and respective linting
* Add `NXF_ANSI_LOG` as global environment variable to template GitHub Actions CI workflow
* Fixed global environment variable in GitHub Actions CI workflow
* Add `--awscli` parameter
* Add `README.txt` path for genomes in `igenomes.config` [nf-core/atacseq#75](https://github.com/nf-core/atacseq/issues/75)
* Fix buggy ANSI codes in pipeline summary log messages
* Add a `TODO` line in the new GitHub Actions CI test files

Expand Down
15 changes: 8 additions & 7 deletions docs/lint_errors.md
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Expand Up @@ -12,9 +12,9 @@ The lint test looks for the following required files:
* The main nextflow config file
* `Dockerfile`
* A docker build script to generate a docker image with the required software
* Continuous integration tests with either [GitHub actions](https://github.com/features/actions), [Travis CI](https://travis-ci.com/) or [Circle CI](https://circleci.com/)
* Continuous integration tests with either [GitHub actions](https://github.com/features/actions) or [Travis CI](https://travis-ci.com/)
* GitHub actions workflows for CI (`.github/workflows/ci.yml`), branch protection (`.github/workflows/branch.yml`) and linting (`.github/workflows/linting.yml`)
* Alternatively, `.travis.yml` or `.circleci/config.yml` continuous testing are still allowed but might be deprecated
* Alternatively, `.travis.yml` continuous integration testing is still allowed but will be deprecated in the near future
* `LICENSE`, `LICENSE.md`, `LICENCE.md` or `LICENCE.md`
* The MIT licence. Copy from [here](https://raw.githubusercontent.com/nf-core/tools/master/LICENSE).
* `README.md`
Expand Down Expand Up @@ -101,8 +101,8 @@ The following variables throw warnings if missing:
* `params.reads`
* Input parameter to specify input data (typically FastQ files / pairs)
* `params.single_end`
* Specify to work with single-end sequence data instead of default paired-end
* Used with Nextflow: `.fromFilePairs( params.reads, size: params.single_end ? 1 : 2 )`
* Specify to work with single-end sequence data instead of paired-end by default
* Nextflow implementation: `.fromFilePairs( params.reads, size: params.single_end ? 1 : 2 )`

The following variables are depreciated and fail the test if they are still present:

Expand All @@ -113,11 +113,12 @@ The following variables are depreciated and fail the test if they are still pres
* `params.container`
* The old method for specifying the dockerhub container address. Replaced by `process.container`
* `singleEnd` and `igenomesIgnore`
* Now using `snake_case` for all command line options
* Changed to `single_end` and `igenomes_ignore`
* The `snake_case` convention should now be used when defining pipeline parameters

## Error #5 - Continuous Integration configuration ## {#5}

nf-core pipelines must have CI testing with GitHub actions, Travis or Circle CI.
nf-core pipelines must have CI testing with GitHub actions or Travis.

This test fails if the following requirements are not met:

Expand All @@ -136,7 +137,7 @@ For GitHub actions CI workflow:
nxf_ver: ['19.10.0', '']
```

* `.github/workflows/ci.yml` must pull the container with the command `docker pull <container>:dev && docker tag <container>:dev <container>:tag` under `jobs`,`test`,`steps`. E.g. for nfcore/tools container:
* `.github/workflows/ci.yml` must pull the container with the command `docker pull <container>:dev && docker tag <container>:dev <container>:<tag>` under `jobs`,`test`,`steps`. E.g. for nfcore/tools container:

```yaml
jobs:
Expand Down
23 changes: 23 additions & 0 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/igenomes.config
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Expand Up @@ -18,6 +18,7 @@ params {
bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt"
mito_name = "MT"
macs_gsize = "2.7e9"
blacklist = "${baseDir}/assets/blacklists/GRCh37-blacklist.bed"
Expand All @@ -42,6 +43,7 @@ params {
bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt"
mito_name = "MT"
macs_gsize = "1.87e9"
blacklist = "${baseDir}/assets/blacklists/GRCm38-blacklist.bed"
Expand All @@ -54,6 +56,7 @@ params {
bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt"
mito_name = "Mt"
}
'EB2' {
Expand All @@ -64,6 +67,7 @@ params {
bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt"
}
'UMD3.1' {
fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
Expand All @@ -73,6 +77,7 @@ params {
bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
mito_name = "MT"
}
'WBcel235' {
Expand All @@ -94,6 +99,7 @@ params {
bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
mito_name = "MT"
}
'GRCz10' {
Expand Down Expand Up @@ -125,6 +131,7 @@ params {
bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
mito_name = "MT"
}
'EB1' {
Expand All @@ -135,6 +142,7 @@ params {
bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt"
}
'Galgal4' {
fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
Expand All @@ -154,6 +162,7 @@ params {
bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
}
'Mmul_1' {
fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
Expand All @@ -163,6 +172,7 @@ params {
bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
mito_name = "MT"
}
'IRGSP-1.0' {
Expand All @@ -183,6 +193,7 @@ params {
bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
mito_name = "MT"
}
'Rnor_6.0' {
Expand Down Expand Up @@ -214,6 +225,7 @@ params {
bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
mito_name = "MT"
macs_gsize = "1.21e7"
}
Expand All @@ -225,6 +237,7 @@ params {
bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
}
'Sscrofa10.2' {
fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
Expand All @@ -234,6 +247,7 @@ params {
bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt"
mito_name = "MT"
}
'AGPv3' {
Expand Down Expand Up @@ -266,6 +280,7 @@ params {
bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt"
mito_name = "chrM"
macs_gsize = "2.7e9"
blacklist = "${baseDir}/assets/blacklists/hg19-blacklist.bed"
Expand All @@ -278,6 +293,7 @@ params {
bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt"
mito_name = "chrM"
macs_gsize = "1.87e9"
blacklist = "${baseDir}/assets/blacklists/mm10-blacklist.bed"
Expand All @@ -300,6 +316,7 @@ params {
bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
mito_name = "chrM"
macs_gsize = "9e7"
}
Expand All @@ -311,6 +328,7 @@ params {
bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
mito_name = "chrM"
}
'danRer10' {
Expand Down Expand Up @@ -342,6 +360,7 @@ params {
bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt"
mito_name = "chrM"
}
'galGal4' {
Expand All @@ -352,6 +371,7 @@ params {
bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
mito_name = "chrM"
}
'panTro4' {
Expand All @@ -362,6 +382,7 @@ params {
bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt"
mito_name = "chrM"
}
'rn6' {
Expand All @@ -380,6 +401,7 @@ params {
bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/"
star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/"
bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/"
readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
mito_name = "chrM"
macs_gsize = "1.2e7"
}
Expand All @@ -391,6 +413,7 @@ params {
bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/"
gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf"
bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed"
readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt"
mito_name = "chrM"
}
}
Expand Down
2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -3,7 +3,7 @@
from setuptools import setup, find_packages
import sys

version = '1.8dev'
version = '1.8'

with open('README.md') as f:
readme = f.read()
Expand Down