diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
index 84250fbe..82521b67 100644
--- a/.github/workflows/awsfulltest.yml
+++ b/.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
diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml
index 5e62f62f..eeab8b33 100644
--- a/.github/workflows/awstest.yml
+++ b/.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
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 464b7f7a..f44099bc 100644
--- a/.github/workflows/ci.yml
+++ b/.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
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 15b83a6a..7a343fe8 100644
--- a/CHANGELOG.md
+++ b/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
 
diff --git a/conf/igenomes.config b/conf/igenomes.config
index caeafceb..088a3a60 100644
--- a/conf/igenomes.config
+++ b/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"
     }
   }
 }
diff --git a/conf/test.config b/conf/test.config
index aa5edfd3..3ae89828 100644
--- a/conf/test.config
+++ b/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'
diff --git a/conf/test_full.config b/conf/test_full.config
index 8461afe9..7a26ee7f 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -12,10 +12,38 @@ params {
   config_profile_description = 'Full test dataset to check pipeline function'
 
   // Input data for full size test
-  // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-  // TODO nf-core: Give any required params for the test so that command line flags are not needed
   input_paths = [
-    ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']],
-    ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']]
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398625_GSM2560978_control_preclinic3_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398623_GSM2560976_control_preclinic1_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398626_GSM2560979_control_preclinic4_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398624_GSM2560977_control_preclinic2_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398627_GSM2560980_control_preclinic5_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398628_GSM2560981_control_preclinic6_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398631_GSM2560984_preclinic3_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398629_GSM2560982_preclinic1_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398630_GSM2560983_preclinic2_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398632_GSM2560985_preclinic4_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398633_GSM2560986_preclinic5_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398634_GSM2560987_preclinic6_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398636_GSM2560989_preclinic7_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398639_GSM2560992_control_clinic3_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398635_GSM2560988_control_preclinic7_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398638_GSM2560991_control_clinic2_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398637_GSM2560990_control_clinic1_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398640_GSM2560993_control_clinic4_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398641_GSM2560994_control_clinic5_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398643_GSM2560996_clinic1_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398642_GSM2560995_control_clinic6_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398644_GSM2560997_clinic2_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398645_GSM2560998_clinic3_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398646_GSM2560999_clinic4_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398649_GSM2561002_control_clinic7_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398647_GSM2561000_clinic5_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398648_GSM2561001_clinic6_Homo_sapiens_ncRNA-Seq.fastq.gz',
+    's3://nf-core-awsmegatests/smrnaseq/input_data/SRR5398650_GSM2561003_clinic7_Homo_sapiens_ncRNA-Seq.fastq.gz'
   ]
+
+  genome = 'GRCh38'
 }
+
+
diff --git a/main.nf b/main.nf
index c6af4bf4..baf6675a 100644
--- a/main.nf
+++ b/main.nf
@@ -78,10 +78,9 @@ if (params.genomes && params.genome && !params.genomes.containsKey(params.genome
 
 // Genome options
 params.bt_index = params.genome ? params.genomes[ params.genome ].bowtie ?: false : false
-params.mature = params.genome ? params.genomes[ params.genome ].mature ?: false : false
-params.hairpin = params.genome ? params.genomes[ params.genome ].hairpin ?: false : false
 params.mirtrace_species = params.genome ? params.genomes[ params.genome ].mirtrace_species ?: false : false
 params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false
+params.mirna_gtf = params.mirtrace_species ? "ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${params.mirtrace_species}.gff3" : false
 
 // Define regular variables so that they can be overwritten
 clip_r1 = params.clip_r1
@@ -114,50 +113,37 @@ if (params.protocol == "illumina"){
     protocol = params.protocol
 }
 
-if (!params.mirna_gtf && params.mirtrace_species){
-    mirna_gtf = file("ftp://mirbase.org/pub/mirbase/CURRENT/genomes/${params.mirtrace_species}.gff3", checkIfExists: true)
-}else if (params.mirna_gtf) {
+if (params.mirna_gtf) {
     mirna_gtf = file(params.mirna_gtf, checkIfExists: true)
-}else{
+} else {
     mirna_gtf = false
 }
 
 // Validate inputs
-
 if (params.skip_mirdeep){
-  if (params.mature) { mature = file(params.mature, checkIfExists: true) } else { exit 1, "Mature file not found: ${params.mature}" }
-  if (params.hairpin) { hairpin = file(params.hairpin, checkIfExists: true) } else { exit 1, "Hairpin file not found: ${params.hairpin}" }
-  if (params.gtf) { gtf = file(params.gtf, checkIfExists: true) }
-  indices_mirdeep2 = Channel.empty()
-  fasta = Channel.empty()
-}
-else{
-  if (params.references_parsed){Channel.empty()
-    fasta = file("$params.references_parsed/genome.fa", checkIfExists: true)
-    hairpin = file("$params.references_parsed/hairpin.fa", checkIfExists: true)
-    mature = file("$params.references_parsed/mature.fa", checkIfExists: true)
-    indices_mirdeep2 = Channel
-    .fromPath("$params.references_parsed/genome.*.ebwt", checkIfExists: true)
-    .ifEmpty { exit 1, "Reference parsed genome indices not found: ${references_parsed}"}
-  }
-  else{
-    if (params.mature) { reference_mature = file(params.mature, checkIfExists: true) } else { exit 1, "Mature file not found: ${params.mature}" }
-    if (params.hairpin) { reference_hairpin = file(params.hairpin, checkIfExists: true) } else { exit 1, "Hairpin file not found: ${params.hairpin}" }
-    if (params.fasta) {reference_genome = file(params.fasta, checkIfExists: true) } else { exit 1, "Reference genome file not found: ${params.fasta}" }
-  }
+    if (params.mature) { mature = file(params.mature, checkIfExists: true) } else { exit 1, "Mature file not found: ${params.mature}" }
+    if (params.hairpin) { hairpin = file(params.hairpin, checkIfExists: true) } else { exit 1, "Hairpin file not found: ${params.hairpin}" }
+    indices_mirdeep2 = Channel.empty()
+    fasta = Channel.empty()
+} else {
+    if (params.references_parsed){
+        fasta = file("$params.references_parsed/genome.fa", checkIfExists: true)
+        hairpin = file("$params.references_parsed/hairpin.fa", checkIfExists: true)
+        mature = file("$params.references_parsed/mature.fa", checkIfExists: true)
+        indices_mirdeep2 = Channel.fromPath("$params.references_parsed/genome.*.ebwt", checkIfExists: true).ifEmpty { exit 1, "Reference parsed genome indices not found: ${references_parsed}"}
+    } else {
+        if (params.mature) { reference_mature = file(params.mature, checkIfExists: true) } else { exit 1, "Mature file not found: ${params.mature}" }
+        if (params.hairpin) { reference_hairpin = file(params.hairpin, checkIfExists: true) } else { exit 1, "Hairpin file not found: ${params.hairpin}" }
+        if (params.fasta) { reference_genome = file(params.fasta, checkIfExists: true) } else { exit 1, "Reference genome file not found: ${params.fasta}" }
+    }
 }
 
 if( params.bt_index ){
-  bt_indices = Channel
-    .fromPath("${params.bt_index}*", checkIfExists: true)
-    .ifEmpty { exit 1, "Bowtie1 index directory not found: ${bt_dir}" }
-}
-
-else if( params.bt_indices ){
-    bt_indices = Channel.from(params.input_paths).map{ file(it) }.toList()
-}
-if( !params.bt_index) {
-    log.info "No GTF / Bowtie 1 index supplied - host reference genome analysis will be skipped."
+    bt_indices = Channel.fromPath("${params.bt_index}*", checkIfExists: true).ifEmpty { exit 1, "Bowtie1 index directory not found: ${bt_dir}" }
+} else if( params.bt_indices ){
+    bt_indices = Channel.from(params.bt_indices).map{ file(it) }.toList()
+} else {
+    log.info "No Bowtie 1 index supplied - host reference genome analysis will be skipped."
 }
 if( !params.mirtrace_species ){
     exit 1, "Reference species for miRTrace is not defined."
@@ -327,9 +313,24 @@ if (!params.references_parsed && !params.skip_mirdeep){
 
     script:
     """
+    # Uncompress FASTA reference files if necessary
+    MATURE="$mature"
+    HAIRPIN="$hairpin"
+    if [ \${MATURE: -3} == ".gz" ]; then
+        gunzip "$mature"
+    fi
+    if [ \${HAIRPIN: -3} == ".gz" ]; then
+        gunzip "$hairpin"
+    fi
+
+    # Remove any special base characters from reference genome FASTA file
     sed -i '/^[^>]/s/[^ATGCatgc]/N/g' $refgenome
+
+    # Remove spaces from miRBase FASTA files
     sed -i 's, ,_,g' $hairpin
     sed -i 's, ,_,g' $mature
+
+    # Build bowtie index
     bowtie-build $refgenome genome
     """
   }
diff --git a/nextflow.config b/nextflow.config
index 277c7b05..a764d210 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -12,7 +12,19 @@ params {
   input = "data/*.fastq.gz"
   outdir = './results'
   protocol = 'illumina'
+
+  // Reference genomes
   genome = false
+  mature = false
+  hairpin = false
+  mirna_gtf = false
+  fasta = false
+  bt_index = false
+  mirtrace_species = false
+  references_parsed = false
+  mature = "ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz"
+  hairpin = "ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz"
+
   clip_r1 = 0
   three_prime_clip_r1 = 0
   three_prime_adapter = "TGGAATTCTCGGGTGCCAAGG"
@@ -23,7 +35,6 @@ params {
   skip_mirdeep = false
   save_reference = true
   seq_center = ""
-  references_parsed = false
 
   // Boilerplate options
   name = false
@@ -85,6 +96,7 @@ profiles {
     podman.enabled = true
   }
   test { includeConfig 'conf/test.config' }
+  test_full { includeConfig 'conf/test_full.config' }
 }
 
 // Load igenomes.config if required
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 6d8825f5..eede33e7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -69,18 +69,28 @@
                 "fasta": {
                     "type": "string",
                     "fa_icon": "fas fa-font",
-                    "description": "Path to FASTA genome file.",
+                    "description": "Path to reference genome FASTA genome file.",
                     "help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
                 },
+                "mirna_gtf": {
+                    "type": "string",
+                    "description": "GFF/GTF file with coordinates positions of precursor and miRNAs.",
+                    "help_text": "miRBase `.gff3` file, typically downloadedfrom [`ftp://mirbase.org/pub/mirbase/CURRENT/genomes/`](ftp://mirbase.org/pub/mirbase/CURRENT/genomes/)\n\nIf using iGenomes with `--genome` this file will be downloaded from miRBase automatically during the pipeline run.\n\n",
+                    "fa_icon": "fas fa-address-book"
+                },
                 "mature": {
                     "type": "string",
                     "description": "Path to FASTA file with mature miRNAs.",
-                    "fa_icon": "fas fa-wheelchair"
+                    "fa_icon": "fas fa-wheelchair",
+                    "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.",
+                    "default": "ftp://mirbase.org/pub/mirbase/CURRENT/mature.fa.gz"
                 },
                 "hairpin": {
                     "type": "string",
                     "description": "Path to FASTA file with miRNAs precursors.",
-                    "fa_icon": "fab fa-cuttlefish"
+                    "fa_icon": "fab fa-cuttlefish",
+                    "help_text": "Typically this will be the `mature.fa` file from miRBase. Can be given either as a plain text `.fa` file or a compressed `.gz` file.\n\nDefaults to the current miRBase release URL, from which the file will be downloaded.",
+                    "default": "ftp://mirbase.org/pub/mirbase/CURRENT/hairpin.fa.gz"
                 },
                 "bt_index": {
                     "type": "string",