Remove .travis.yml and fix a couple of issues

CHANGELOG.md

@@ -9,14 +9,16 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-* [#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!
+* [nf-core/atacseq#63](https://github.com/nf-core/atacseq/issues/63) - Added multicore support for Trim Galore!
+* [nf-core/atacseq#75](https://github.com/nf-core/atacseq/issues/75) - Include gene annotation versions in multiqc report
+* [nf-core/atacseq#76](https://github.com/nf-core/atacseq/issues/76) - featureCounts coupled to DESeq2
 * Added GitHub Actions CI tests
 
 ### `Fixed`
 
 * [#118](https://github.com/nf-core/chipseq/issues/118) - Running on with SGE
 * [#132](https://github.com/nf-core/chipseq/issues/132) - BigWig Error: sort: cannot create temporary file in '': Read-only file system
-* [#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
+* [nf-core/atacseq#73](https://github.com/nf-core/atacseq/issues/73) - macs_annotatePeaks.mLb.clN.summary.txt file is not created
 * Make executables in `bin/` compatible with Python 3
 
 ### `Dependencies`
@@ -56,7 +58,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Added`
 
-* [#46](https://github.com/nf-core/atacseq/issues/46) - Missing gene_bed path in igenomes config
+* [nf-core/atacseq#46](https://github.com/nf-core/atacseq/issues/46) - Missing gene_bed path in igenomes config
 * Update template to tools `1.7`
 * Add `--trim_nextseq` parameter
 * Add `CITATIONS.md` file
@@ -65,10 +67,10 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Fixed`
 
 * **Change all parameters from `camelCase` to `snake_case` (see [Deprecated](#Deprecated))**
-* [#44](https://github.com/nf-core/atacseq/issues/44) - Output directory missing: macs2/consensus/deseq2
-* [#45](https://github.com/nf-core/atacseq/issues/45) - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
-* [#46](https://github.com/nf-core/atacseq/issues/46) - Stage blacklist file in channel properly
-* [#50](https://github.com/nf-core/atacseq/issues/50) - HOMER number of peaks does not correspond to found MACS2 peaks
+* [nf-core/atacseq#44](https://github.com/nf-core/atacseq/issues/44) - Output directory missing: macs2/consensus/deseq2
+* [nf-core/atacseq#45](https://github.com/nf-core/atacseq/issues/45) - Wrong x-axis scale for the HOMER: Peak annotation Counts tab plot?
+* [nf-core/atacseq#46](https://github.com/nf-core/atacseq/issues/46) - Stage blacklist file in channel properly
+* [nf-core/atacseq#50](https://github.com/nf-core/atacseq/issues/50) - HOMER number of peaks does not correspond to found MACS2 peaks
 * Fixed bug in UpSetR peak intersection plot
 * Increase default resource requirements in `base.config`
 * Increase process-specific requirements based on user-reported failures

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.7
+FROM nfcore/base:1.8
 LABEL authors="Philip Ewels" \
       description="Docker image containing all software requirements for the nf-core/chipseq pipeline"
 

README.md

@@ -1,6 +1,5 @@
 # ![nf-core/chipseq](docs/images/nf-core-chipseq_logo.png)
 
-[![Build Status](https://travis-ci.com/nf-core/chipseq.svg?branch=master)](https://travis-ci.com/nf-core/chipseq)
 [![GitHub Actions CI Status](https://github.com/nf-core/chipseq/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/chipseq/actions)
 [![GitHub Actions Linting Status](https://github.com/nf-core/chipseq/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/chipseq/actions)
 [![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A519.10.0-brightgreen.svg)](https://www.nextflow.io/)

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"
     }
   }