Add s3 data paths to test_full.config

.github/workflows/awsfulltest.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7

.github/workflows/awstest.yml

@@ -13,7 +13,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Setup Miniconda
-        uses: goanpeca/setup-miniconda@v1.0.2
+        uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: 3.7

.github/workflows/ci.yml

@@ -26,9 +26,9 @@ jobs:
         uses: actions/checkout@v2
 
       - name: Check if Dockerfile or Conda environment changed
-        uses: technote-space/get-diff-action@v1
+        uses: technote-space/get-diff-action@v4
         with:
-          PREFIX_FILTER: |
+          FILES: |
             Dockerfile
             environment.yml
 

CHANGELOG.md

@@ -15,6 +15,10 @@
 * Update conda environment with new packages and updates
 * Added `--protocol custom` to allow custom adapter trimming modes [[#41]](https://github.com/nf-core/smrnaseq/issues/41)]
 * Fix error when UMI is on the reads header: [[#35](https://github.com/nf-core/smrnaseq/issues/35)]
+* Updated `params.mirtrace_species` to be properly initialised when using `--genome`, for all iGenomes species
+* Made `params.mature` and `params.hairpin` default to miRBase FTP URL so that the file is automatically downloaded if not provided
+* Allow `.fa` or `.fa.gz` files for mature and hairpin FASTA files.
+* Add full-size benchmark / test dataset to run on AWS for each release (see `test_full.config`)
 
 ### Packaged software updates
 

conf/igenomes.config

@@ -22,6 +22,7 @@ params {
       mito_name   = "MT"
       macs_gsize  = "2.7e9"
       blacklist   = "${baseDir}/assets/blacklists/GRCh37-blacklist.bed"
+      mirtrace_species = "hsa"
     }
     'GRCh38' {
       fasta       = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa"
@@ -34,6 +35,7 @@ params {
       mito_name   = "chrM"
       macs_gsize  = "2.7e9"
       blacklist   = "${baseDir}/assets/blacklists/hg38-blacklist.bed"
+      mirtrace_species = "hsa"
     }
     'GRCm38' {
       fasta       = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa"
@@ -47,6 +49,7 @@ params {
       mito_name   = "MT"
       macs_gsize  = "1.87e9"
       blacklist   = "${baseDir}/assets/blacklists/GRCm38-blacklist.bed"
+      mirtrace_species = "mmu"
     }
     'TAIR10' {
       fasta       = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa"
@@ -58,6 +61,7 @@ params {
       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"
+      mirtrace_species = "ath"
     }
     'EB2' {
       fasta       = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa"
@@ -68,6 +72,7 @@ params {
       gtf         = "${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"
+      // mirtrace_species = "bsu"
     }
     'UMD3.1' {
       fasta       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa"
@@ -79,6 +84,7 @@ params {
       bed12       = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed"
       readme      = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt"
       mito_name   = "MT"
+      mirtrace_species = "bta"
     }
     'WBcel235' {
       fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa"
@@ -90,6 +96,7 @@ params {
       bed12       = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed"
       mito_name   = "MtDNA"
       macs_gsize  = "9e7"
+      mirtrace_species = "cel"
     }
     'CanFam3.1' {
       fasta       = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa"
@@ -101,6 +108,7 @@ params {
       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"
+      mirtrace_species = "cfa"
     }
     'GRCz10' {
       fasta       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa"
@@ -111,6 +119,7 @@ params {
       gtf         = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf"
       bed12       = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed"
       mito_name   = "MT"
+      mirtrace_species = "dre"
     }
     'BDGP6' {
       fasta       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa"
@@ -122,6 +131,7 @@ params {
       bed12       = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed"
       mito_name   = "M"
       macs_gsize  = "1.2e8"
+      mirtrace_species = "dme"
     }
     'EquCab2' {
       fasta       = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa"
@@ -133,6 +143,7 @@ params {
       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"
+      // mirtrace_species = "ecb"
     }
     'EB1' {
       fasta       = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa"
@@ -143,6 +154,7 @@ params {
       gtf         = "${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"
+      // mirtrace_species = "ecd"
     }
     'Galgal4' {
       fasta       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa"
@@ -153,6 +165,7 @@ params {
       gtf         = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf"
       bed12       = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed"
       mito_name   = "MT"
+      mirtrace_species = "gga"
     }
     'Gm01' {
       fasta       = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa"
@@ -163,6 +176,7 @@ params {
       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      = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt"
+      // mirtrace_species = "gmx"
     }
     'Mmul_1' {
       fasta       = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa"
@@ -174,6 +188,7 @@ params {
       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"
+      // mirtrace_species = "mcc"
     }
     'IRGSP-1.0' {
       fasta       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa"
@@ -184,6 +199,7 @@ params {
       gtf         = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf"
       bed12       = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed"
       mito_name   = "Mt"
+      mirtrace_species = "osa"
     }
     'CHIMP2.1.4' {
       fasta       = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa"
@@ -195,6 +211,7 @@ params {
       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"
+      mirtrace_species = "ptr"
     }
     'Rnor_6.0' {
       fasta       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa"
@@ -205,6 +222,7 @@ params {
       gtf         = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf"
       bed12       = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed"
       mito_name   = "MT"
+      mirtrace_species = "rno"
     }
     'R64-1-1' {
       fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa"
@@ -216,6 +234,7 @@ params {
       bed12       = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed"
       mito_name   = "MT"
       macs_gsize  = "1.2e7"
+      // mirtrace_species = "sce"
     }
     'EF2' {
       fasta       = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa"
@@ -228,6 +247,7 @@ params {
       readme      = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt"
       mito_name   = "MT"
       macs_gsize  = "1.21e7"
+      // mirtrace_species = "spo"
     }
     'Sbi1' {
       fasta       = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa"
@@ -238,6 +258,7 @@ params {
       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      = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt"
+      mirtrace_species = "sbi"
     }
     'Sscrofa10.2' {
       fasta       = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa"
@@ -249,6 +270,7 @@ params {
       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"
+      mirtrace_species = "ssc"
     }
     'AGPv3' {
       fasta       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa"
@@ -259,6 +281,7 @@ params {
       gtf         = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf"
       bed12       = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed"
       mito_name   = "Mt"
+      mirtrace_species = "zma"
     }
     'hg38' {
       fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa"
@@ -271,6 +294,7 @@ params {
       mito_name   = "chrM"
       macs_gsize  = "2.7e9"
       blacklist   = "${baseDir}/assets/blacklists/hg38-blacklist.bed"
+      mirtrace_species = "hsa"
     }
     'hg19' {
       fasta       = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
@@ -284,6 +308,7 @@ params {
       mito_name   = "chrM"
       macs_gsize  = "2.7e9"
       blacklist   = "${baseDir}/assets/blacklists/hg19-blacklist.bed"
+      mirtrace_species = "hsa"
     }
     'mm10' {
       fasta       = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa"
@@ -297,6 +322,7 @@ params {
       mito_name   = "chrM"
       macs_gsize  = "1.87e9"
       blacklist   = "${baseDir}/assets/blacklists/mm10-blacklist.bed"
+      mirtrace_species = "mmu"
     }
     'bosTau8' {
       fasta       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa"
@@ -307,6 +333,7 @@ params {
       gtf         = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf"
       bed12       = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed"
       mito_name   = "chrM"
+      mirtrace_species = "bta"
     }
     'ce10' {
       fasta       = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa"
@@ -319,6 +346,7 @@ params {
       readme      = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt"
       mito_name   = "chrM"
       macs_gsize  = "9e7"
+      mirtrace_species = "cel"
     }
     'canFam3' {
       fasta       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa"
@@ -330,6 +358,7 @@ params {
       bed12       = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed"
       readme      = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt"
       mito_name   = "chrM"
+      mirtrace_species = "cfa"
     }
     'danRer10' {
       fasta       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa"
@@ -341,6 +370,7 @@ params {
       bed12       = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed"
       mito_name   = "chrM"
       macs_gsize  = "1.37e9"
+      mirtrace_species = "dre"
     }
     'dm6' {
       fasta       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa"
@@ -352,6 +382,7 @@ params {
       bed12       = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed"
       mito_name   = "chrM"
       macs_gsize  = "1.2e8"
+      mirtrace_species = "dme"
     }
     'equCab2' {
       fasta       = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa"
@@ -363,6 +394,7 @@ params {
       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"
+      // mirtrace_species = "ecb"
     }
     'galGal4' {
       fasta       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa"
@@ -374,6 +406,7 @@ params {
       bed12       = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed"
       readme      = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt"
       mito_name   = "chrM"
+      mirtrace_species = "gga"
     }
     'panTro4' {
       fasta       = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa"
@@ -385,6 +418,7 @@ params {
       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"
+      mirtrace_species = "ptr"
     }
     'rn6' {
       fasta       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa"
@@ -395,6 +429,7 @@ params {
       gtf         = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf"
       bed12       = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed"
       mito_name   = "chrM"
+      mirtrace_species = "rno"
     }
     'sacCer3' {
       fasta       = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa"
@@ -405,6 +440,7 @@ params {
       readme      = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt"
       mito_name   = "chrM"
       macs_gsize  = "1.2e7"
+      // mirtrace_species = "sce"
     }
     'susScr3' {
       fasta       = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa"
@@ -416,6 +452,7 @@ params {
       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"
+      mirtrace_species = "ssc"
     }
   }
 }

conf/test.config

@@ -29,7 +29,7 @@ params {
     'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.4.ebwt',
     'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.rev.1.ebwt',
     'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.rev.1.ebwt'
-]
+  ]
   gtf = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genes.gtf'
   mature = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/mature.fa'
   hairpin = 'https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hairpin.fa'