Merge pull request #483 from drpatelh/master

Fix a couple of things in CHANGELOG

CHANGELOG.md

@@ -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
@@ -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
@@ -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
 

docs/lint_errors.md

@@ -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`
@@ -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:
 
@@ -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:
 
@@ -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:

nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/igenomes.config

@@ -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   = "${baseDir}/assets/blacklists/GRCh37-blacklist.bed"
@@ -42,6 +43,7 @@ params {
       bismark     = "${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"
@@ -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' {
@@ -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       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
@@ -73,6 +77,7 @@ params {
       bismark     = "${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      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
       mito_name   = "MT"
     }
     'WBcel235' {
@@ -94,6 +99,7 @@ params {
       bismark     = "${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      = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt"
       mito_name   = "MT"
     }
     'GRCz10' {
@@ -125,6 +131,7 @@ params {
       bismark     = "${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      = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt"
       mito_name   = "MT"
     }
     'EB1' {
@@ -135,6 +142,7 @@ params {
       bismark     = "${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"
@@ -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       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
@@ -163,6 +172,7 @@ params {
       bismark     = "${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      = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt"
       mito_name   = "MT"
     }
     'IRGSP-1.0' {
@@ -183,6 +193,7 @@ params {
       bismark     = "${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      = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt"
       mito_name   = "MT"
     }
     'Rnor_6.0' {
@@ -214,6 +225,7 @@ params {
       bismark     = "${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      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
       mito_name   = "MT"
       macs_gsize  = "1.21e7"
     }
@@ -225,6 +237,7 @@ params {
       bismark     = "${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"
@@ -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' {
@@ -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   = "${baseDir}/assets/blacklists/hg19-blacklist.bed"
@@ -278,6 +293,7 @@ params {
       bismark     = "${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"
@@ -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"
     }
@@ -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' {
@@ -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' {
@@ -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' {
@@ -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' {
@@ -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"
     }
@@ -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"
     }
   }

setup.py

@@ -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()