diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 6e833767..3996d01d 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -74,6 +74,7 @@ jobs:
             "test_contrast_list",
             "test_no_multiqc",
             "test_relevel",
+            "test_smrnaseq",
             "test_star_rsem",
             "test_star_salmon",
             "test_use_vst",
diff --git a/.prettierignore b/.prettierignore
index 437d763d..88a6ffb4 100644
--- a/.prettierignore
+++ b/.prettierignore
@@ -6,6 +6,7 @@ work/
 data/
 results/
 .DS_Store
+testdata/
 testing/
 testing*
 *.pyc
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 2b5292b6..e07a79a6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
+- [#213](https://github.com/qbic-pipelines/rnadeseq/pull/21) Added smrnaseq input support
 - [#212](https://github.com/qbic-pipelines/rnadeseq/pull/212) Added computational methods if no --software_versions
 - [#206](https://github.com/qbic-pipelines/rnadeseq/pull/206) Added logic to decide between rlog and vst, added tryCatch for heatmap saving because this only works unreliably
 - [#202](https://github.com/qbic-pipelines/rnadeseq/pull/202) Added background list to pathway analysis
diff --git a/assets/RNAseq_report.Rmd b/assets/RNAseq_report.Rmd
index 0fe78896..8d3d3135 100644
--- a/assets/RNAseq_report.Rmd
+++ b/assets/RNAseq_report.Rmd
@@ -86,6 +86,35 @@ label_size <- function(dimension_int) {
     val <- max(c(2, 10-dimension_int/15))
     return(val)
 }
+
+# Function for creating a dataframe from smrnaseq files
+build_smrnaseq_df <- function(files) {
+    merged_mat <- F
+    for (f in files) {
+        file_tab <- read.table(f, sep="\t", row.names=1)
+        # Usually, the last row is weird and has the rowname *, remove it
+        if (grep("*", tail(rownames(file_tab), n=1), fixed=T)) {
+            file_tab <- head(file_tab, -1)
+        }
+
+        # If merged_mat already exists, add third matrix column to it (second column after rownames)
+        if (is.data.frame(merged_mat)) {
+
+            # Check if rownames are the same
+            if (rownames(file_tab) != rownames(merged_mat)) {
+                stop(paste("Rownames of smrnaseq file", file_tab, "differ from the rownames of the other files; exiting..."))
+            }
+            merged_mat[[basename(f)]] <- file_tab[,2]
+        } else {
+
+            # Otherwise initiate it from third matrix column and rownames
+            merged_mat <- data.frame(file_tab[,2])
+            rownames(merged_mat) <- rownames(file_tab)
+            colnames(merged_mat) <- c(basename(f))
+        }
+    }
+    merged_mat
+}
 ```
 
 ```{r param_validation, echo=FALSE, message=FALSE, warning=FALSE, results = 'hide'}
@@ -159,8 +188,8 @@ write_error_msg <- function(counts, qbicCodes) {
 }
 
 #Check necessary params
-if (!(params$input_type %in% c("featurecounts", "rsem", "salmon"))){
-    stop(paste0("Wrong input type ", params$input_type, ", must be one of [featurecounts, rsem, salmon]!"))
+if (!(params$input_type %in% c("featurecounts", "rsem", "salmon", "smrnaseq"))){
+    stop(paste0("Wrong input type ", params$input_type, ", must be one of [featurecounts, rsem, salmon, smrnaseq]!"))
 }
 if (params$input_type %in% c("rsem", "salmon") & !isProvided(params$path_gtf)){
     stop(paste0("For input type salmon, gtf file needs to be provided!\nIf using igenomes, please check that the entry for your genome contains a gtf file and otherwise provide one with `--gtf`."))
@@ -340,9 +369,60 @@ metadata$sampleName = paste(row.names(metadata),metadata$Secondary.Name,sep="_")
 row.names(metadata) = metadata$sampleName
 metadata_save <- metadata
 
+if (params$input_type == "smrnaseq") {
+
+    # Prepare files from smrnaseq, start with hairpins
+    hairpin_files <- file.path(gsub("/$", "", params$path_gene_counts), paste0(qbicCodes, "_mature_hairpin.sorted.idxstats"))
+    if (!(all(file.exists(hairpin_files)))) {
+        missing_files <- "Could not find all of the specified <QBiC-code>_mature_hairpin.sorted.idxstats files! Please check that for all QBiC codes in the metadata sheet, a <QBiC-code>_mature_hairpin.sorted.idxstats file is present in the gene_counts folder and make sure that no typos exist. The following file(s) could not be found: "
+        for (f in hairpin_files) {
+            if (!file.exists(f)) {
+                missing_files <- paste0(missing_files, f, ", ")
+            }
+        }
+        missing_files <- paste0(substring(missing_files, 1, nchar(missing_files)-2), ".")
+        stop(missing_files, call.=F)
+    }
+
+    # Non-hairpins next
+    other_files <- file.path(gsub("/$", "", params$path_gene_counts), paste0(qbicCodes, "_mature.sorted.idxstats"))
+    if (!(all(file.exists(other_files)))) {
+        missing_files <- "Could not find all of the specified <QBiC-code>_mature.sorted.idxstats files! Please check that for all QBiC codes in the metadata sheet, a <QBiC-code>_mature.sorted.idxstats file is present in the gene_counts folder and make sure that no typos exist. The following file(s) could not be found: "
+        for (f in other_files) {
+            if (!file.exists(f)) {
+                missing_files <- paste0(missing_files, f, ", ")
+            }
+        }
+        missing_files <- paste0(substring(missing_files, 1, nchar(missing_files)-2), ".")
+        stop(missing_files, call.=F)
+    }
+    
+    # Combine files for later
+    files <- c(hairpin_files, other_files)
+
+    # Merge hairpins and counts
+    hairpin_df <- build_smrnaseq_df(hairpin_files)
+    other_df <- build_smrnaseq_df(other_files)
+    colnames(other_df) <- colnames(hairpin_df)
+    count.table <- rbind(hairpin_df, other_df)
+
+    # Need to order columns in count.table
+    count.table <- count.table[, order(names(count.table))]
+
+    count.table$Ensembl_ID <- rownames(count.table)
+    count.table <- cbind(Ensembl_ID=rownames(count.table), gene_name=rownames(count.table), count.table)
+    write.table(count.table, paste("differential_gene_expression/gene_counts_tables/raw_gene_counts.tsv",sep=""), append = FALSE, quote = FALSE, sep = "\t",eol = "\n", na = "NA", dec = ".", row.names = F, qmethod = c("escape", "double"))
+
+
+}
+
 # Load count table for FeatureCounts
 if (params$input_type == "featurecounts"){
     count.table <- read.table(params$path_gene_counts,  header = T,sep = "\t",na.strings =c("","NA"),quote=NULL,stringsAsFactors=F,dec=".",fill=TRUE,row.names=1)
+}
+
+# Processing is the same for FeatureCounts and the smrnaseq matrix that is built above
+if (params$input_type %in% c("featurecounts", "smrnaseq")) {
     count.table$Ensembl_ID <- row.names(count.table)
     drop <- c("Ensembl_ID","gene_name")
     gene_names <- count.table[,drop]
@@ -361,8 +441,8 @@ if (params$input_type == "featurecounts"){
     count.table <- count.table[, order(names(count.table))]
 
     if (!identical(names(count.table),qbicCodes)) {
-    error_out <- write_error_msg(count.table, qbicCodes)
-    stop(paste0(error_out, "\n"), call.=F)
+        error_out <- write_error_msg(count.table, qbicCodes)
+        stop(paste0(error_out, "\n"), call.=F)
     }
     names(count.table) = metadata$sampleName
 
@@ -443,7 +523,7 @@ DT::datatable(df_QA_neat, options = list(scrollX  = "100%", scrollY = "400px", p
 
 ################## RUN DESEQ2 ######################################
 # Run DESeq function
-if (params$input_type == "featurecounts") {
+if (params$input_type %in% c("featurecounts", "smrnaseq")) {
     cds <- DESeqDataSetFromMatrix( countData =count.table, colData =metadata, design = eval(parse(text=as.character(design[[1]]))))
 } else if (params$input_type %in% c("rsem", "salmon")) {
     ## Create a dataframe which consists of both the gene id and the transcript name
@@ -469,7 +549,7 @@ if (params$input_type == "featurecounts") {
         #-->the sample name is in the file name
         files <- file.path(gsub("/$", "", params$path_gene_counts), paste0(qbicCodes, ".genes.results"))
         if (!(all(file.exists(files)))) {
-            missing_files <- "DESeq2.R could not find all of the specified <QBiC-code>.genes.results files! Please check that for all QBiC codes in the metadata sheet, a <QBiC-code>.genes.results file is present in the gene_counts folder and make sure that no typos exist. The following file(s) could not be found: "
+            missing_files <- "Could not find all of the specified <QBiC-code>.genes.results files! Please check that for all QBiC codes in the metadata sheet, a <QBiC-code>.genes.results file is present in the gene_counts folder and make sure that no typos exist. The following file(s) could not be found: "
             for (f in files) {
                 if (!file.exists(f)) {
                     missing_files <- paste0(missing_files, f, ", ")
@@ -507,7 +587,7 @@ if (params$input_type == "featurecounts") {
         #-->the sample name is in the subfolder name, not in the file name!
         files <- file.path(gsub("/$", "", params$path_gene_counts), qbicCodes, "quant.sf")
         if (!(all(file.exists(files)))) {
-            missing_files <- "DESeq2.R could not find all of the specified <QBiC-code>/quant.sf files! Please check that for all QBiC codes in the metadata sheet, a <QBiC-code>/quant.sf file is present in the gene_counts folder and <QBiC-code> subfolder and make sure that no typos exist. The following file(s) could not be found: "
+            missing_files <- "Could not find all of the specified <QBiC-code>/quant.sf files! Please check that for all QBiC codes in the metadata sheet, a <QBiC-code>/quant.sf file is present in the gene_counts folder and <QBiC-code> subfolder and make sure that no typos exist. The following file(s) could not be found: "
             for (f in files) {
                 if (!file.exists(f)) {
                     missing_files <- paste0(missing_files, f, ", ")
@@ -533,7 +613,7 @@ if (params$input_type == "featurecounts") {
         cds <- DESeqDataSetFromTximport(txi=txi.salmon, colData =coldata, design = eval(parse(text=as.character(design[[1]]))))
     }
 } else {
-    stop(paste0("Invalid input type: ", params$input_type, "! Input type must be one of: featurecounts, rsem, salmon!"))
+    stop(paste0("Invalid input type: ", params$input_type, "! Input type must be one of: featurecounts, rsem, salmon, smrnaseq!"))
 }
 
 #Apply relevel if provided; this must be done before calling DESeq()
@@ -550,7 +630,7 @@ if (isProvided(params$path_relevel)) {
 cds <- DESeq(cds)
 
 # sizeFactors(cds) as indicator of library sequencing depth
-if (params$input_type == "featurecounts") {
+if (params$input_type %in% c("featurecounts", "smrnaseq")) {
     sf <- sizeFactors(cds)
 } else {
     # If tximport was used, sizeFactors doesn't work, so use workaround as described here: https://support.bioconductor.org/p/97676/
@@ -562,6 +642,11 @@ write.table(sf,paste("differential_gene_expression/gene_counts_tables/sizeFactor
 # Write cds assay table to file
 write.table(counts(cds, normalized=T), paste0("differential_gene_expression/gene_counts_tables/deseq2_library_scaled_gene_counts.tsv"), append=F, quote = F, sep = "\t", eol = "\n", na = "NA", dec = ".", row.names = T, col.names = T, qmethod = c("escape", "double"))
 
+# Or for smrnaseq save folder/file names to txt file
+if (params$input_type == "smrnaseq") {
+    write(files, file="differential_gene_expression/metadata/smrnaseq_files.txt")
+}
+
 # Or for rsem/salmon save folder/file names to txt file
 if (params$input_type == "rsem") {
     write(files, file="differential_gene_expression/metadata/star_rsem_files.txt")
@@ -1273,7 +1358,7 @@ if (isProvided(params$path_contrast_pairs)) {
         write.table(DE_genes_contrast_genename, file=paste("differential_gene_expression/allgenes/DE_contrast_",contname,".tsv",sep=""), sep="\t", quote=F, col.names = T, row.names = F)
 
         # Select only significantly DE
-        DE_genes_contrast <- subset(DE_genes_contrast_genename, padj <= params$adj_pval_threshold & abs(log2FoldChange) >= params$logFC_threshold)
+        DE_genes_contrast <-  subset(DE_genes_contrast_genename, padj <= params$adj_pval_threshold & abs(log2FoldChange) >= params$logFC_threshold)
         DE_genes_contrast <- DE_genes_contrast[order(DE_genes_contrast$padj),]
 
         # Round table before writing
@@ -1294,7 +1379,8 @@ if (isProvided(params$path_contrast_pairs)) {
 # Calculating DE genes for default contrasts (no contrast matrix or list or pairs provided)
 if (!isProvided(params$path_contrast_matrix) & !isProvided(params$path_contrast_list) & !isProvided(params$path_contrast_pairs)) {
     contrast_names <- coefficients[2:length(coefficients)]
-    contrast_names <- contrast_names[!startsWith(contrast_names, "batch_")]
+    contrast_names <- contrast_names[!startsWith(contrast_names, "batch")]
+
     for (contname in contrast_names) {
 
         results_DEseq_contrast <- results(cds, name=contname)
@@ -1313,7 +1399,7 @@ if (!isProvided(params$path_contrast_matrix) & !isProvided(params$path_contrast_
         write.table(DE_genes_contrast_genename, file=paste("differential_gene_expression/allgenes/DE_contrast_",contname,".tsv",sep=""), sep="\t", quote=F, col.names = T, row.names = F)
 
         # Select only significantly DE
-        DE_genes_contrast <- subset(DE_genes_contrast_genename, padj <= params$adj_pval_threshold & abs(log2FoldChange) >= params$logFC_threshold)
+        DE_genes_contrast <-  subset(DE_genes_contrast_genename, padj <= params$adj_pval_threshold & abs(log2FoldChange) >= params$logFC_threshold)
         DE_genes_contrast <- DE_genes_contrast[order(DE_genes_contrast$padj),]
         # Round table before writing
         if (isProvided(params$round_DE) && params$round_DE>-1) {
@@ -1695,7 +1781,7 @@ for (file in contrast_files){
     if (isProvided(params$set_background)) {
         gostres <- gost(query=q,
             organism=gost_id,
-            significant=TRUE,
+            significant=T,
             correction_method="fdr",
             sources=datasources,
             evcodes=TRUE,
@@ -1711,7 +1797,7 @@ for (file in contrast_files){
         # Also run without bg for Venn diagrams
         gostres_nobg <- gost(query=q,
             organism=gost_id,
-            significant=TRUE,
+            significant=T,
             correction_method="fdr",
             sources=datasources,
             evcodes=TRUE,
@@ -1725,7 +1811,7 @@ for (file in contrast_files){
     } else {
         gostres <- gost(query=q,
             organism=gost_id,
-            significant=TRUE,
+            significant=T,
             correction_method="fdr",
             sources=datasources,
             evcodes=TRUE,
@@ -2109,6 +2195,7 @@ and the subfolder: `pathway_heatmaps`.
 # Summary and outlook
 
 ```{r quote, echo=FALSE, results='asis'}
+
 # Only add hyperlink to quote file if it was provided in the params
 quote_string <- ifelse(
     isProvided(params$path_quote),
@@ -2150,6 +2237,10 @@ if (software_versions_csv) {
         quant_tool <- "Salmon"
         quant_version <- as.character(version["SALMON_QUANT"][[1]]["salmon"])
         quant_cite <- "[@patro2017salmon]"
+    } else if (params$input_type == "smrnaseq") {
+        quant_tool <- "SAMtools"
+        quant_version <- as.character(version["SAMTOOLS_IDXSTATS"][[1]]["samtools"])
+        quant_cite <- "[@li2009sequence; @li2011statistical]"
     }
 }
 ```
@@ -2164,23 +2255,50 @@ cat("No software versions file was provided for primary analysis.")
 
 ```{r software_versions_RNASeq, echo=FALSE, results='asis', eval=isProvided(params$path_software_versions)}
 
-# In the following part, I use newlines (in code) where possible whenever the paste0 function switches from a string to a variable call to better distinguish between the two so it is obvious in which lines quotes are needed and in which not --> Cannot always use newlines as this sometimes translates into the report.html
-
+# In the following part, I use newlines (in code) where possible whenever the paste0 function switches from a string to a variable call to better distinguish between the two so it is clearer in which lines quotes are needed and in which not --> Cannot always use newlines as this sometimes translates into the report.html
+# TODO remove F!
+if (params$input_type == "featurecounts" & F){
+    cat(paste0(
+    "## RNAseq data analysis
+
+    The Nextflow-based nf-core pipeline `rnaseq ", as.character(ifelse(software_versions_csv, version["nf-core/rnaseq"], version["Workflow"][[1]]["nf-core/rnaseq"])),
+    "` [^1] was used for the RNAseq Bioinfomatics analysis. `FASTQC ",
+    as.character(ifelse(software_versions_csv, version["FastQC"], version["FASTQC"][[1]]["fastqc"])),
+    "` [^3] [@andrews2010fastqc] was used to determine quality of the FASTQ files.
+    Subsequently, adapter trimming was conducted with `Trim Galore ",
+    as.character(ifelse(software_versions_csv, version["Trim Galore!"], version["TRIMGALORE"][[1]]["trimgalore"])),
+    "` [^4] [@krueger2012trim]. `STAR v",
+    as.character(ifelse(software_versions_csv, substring((version["STAR"]), 7, ), version["MAKE_TRANSCRIPTS_FASTA"][[1]]["star"])),
+    "` [@Dobin2013] aligner was used to map the reads that passed the quality control to the reference genome.
+    The RNA-seq data quality control was performed with `RSeQC ",
+    as.character(ifelse(software_versions_csv, version["RSeQC"], version["RSEQC_BAMSTAT"][[1]]["rseqc"])),
+    "` [@wang2012rseqc] and read quantification of the features (e.g. genes) with `",
+    quant_tool,
+    " ",
+    quant_version,
+    "` ",
+    quant_cite,
+    "."
+    ))
+} else if (params$input_type == "smrnaseq"){
 cat(paste0(
-"## RNAseq data analysis
-    
-The Nextflow-based nf-core pipeline `rnaseq ", as.character(ifelse(software_versions_csv, version["nf-core/rnaseq"], version["Workflow"][[1]]["nf-core/rnaseq"])),
-"` [^1] was used for the RNAseq Bioinfomatics analysis. `FASTQC ",
-as.character(ifelse(software_versions_csv, version["FastQC"], version["FASTQC"][[1]]["fastqc"])),
-"` [^3] [@andrews2010fastqc] was used to determine quality of the FASTQ files.
-Subsequently, adapter trimming was conducted with `Trim Galore ",
-as.character(ifelse(software_versions_csv, version["Trim Galore!"], version["TRIMGALORE"][[1]]["trimgalore"])),
-"` [^4] [@krueger2012trim]. `STAR v",
-as.character(ifelse(software_versions_csv, substring((version["STAR"]), 7, ), version["MAKE_TRANSCRIPTS_FASTA"][[1]]["star"])),
-"` [@Dobin2013] aligner was used to map the reads that passed the quality control to the reference genome.
-The RNA-seq data quality control was performed with `RSeQC ",
-as.character(ifelse(software_versions_csv, version["RSeQC"], version["RSEQC_BAMSTAT"][[1]]["rseqc"])),
-"` [@wang2012rseqc] and read quantification of the features (e.g. genes) with `",
+"## smRNA-seq data analysis
+
+The Nextflow-based nf-core pipeline `smrnaseq ", as.character(version["Workflow"][[1]]["nf-core/smrnaseq"]),
+"` [^6] was used for the smRNA-seq Bioinfomatics analysis. `FASTQC ",
+as.character(version["FASTQC"][[1]]["fastqc"]),
+"` [^3] [@andrews2010fastqc] was used to determine the quality of the miRNA samples. ",
+ifelse("TRIMGALORE" %in% names(version), paste0("Subsequently, adapter trimming was conducted with `Trim Galore ",
+as.character(version["TRIMGALORE"][[1]]["trimgalore"]),
+"` [^4] [@krueger2012trim]."),
+    ifelse("FASTP" %in% names(version), paste0("Subsequently, adapter trimming was conducted with `fastP ",
+    as.character(version["FASTP"][[1]]["fastp"]),
+    "` [^7] [@chen2018fastp; @chen2023ultrafast]."),
+        "")),
+" `Bowtie v", as.character(version["BOWTIE_MAP_HAIRPIN"][[1]]["bowtie"]), "` [@langmead2009ultrafast] aligner was used to map the reads that passed the quality control to the reference database.
+The smRNA-seq data quality control was performed with `miRTrace ",
+as.character(version["MIRTRACE_RUN"][[1]]["mirtrace"]),
+"` [^8] [@kang2018mirtrace] and read quantification of the features (e.g. genes) with `",
 quant_tool,
 " ",
 quant_version,
@@ -2188,15 +2306,14 @@ quant_version,
 quant_cite,
 "."
 ))
+}
+```
 
-```{r MQC_cite, echo=FALSE, results='asis', eval=software_versions_csv&isProvided(params$path_software_versions)}
-
+```{r MQC_cite, echo=FALSE, results='asis', eval=dir.exists(paste0(wd,"/QC/multiqc_data/"))&software_versions_csv&isProvided(params$path_software_versions)}
 cat(paste0("\nAn aggregation of the quality control for the RNAseq analysis was performed with `MultiQC ", as.character(version["MultiQC"]), "` [^2] [@ewels2016multiqc]."))
-
 ```
 
 ```{r software_versions_DE, echo=FALSE, results='asis'}
-
 cat(paste0(
 "## Differential gene expression analysis
 
@@ -2263,3 +2380,6 @@ sessioninfo::session_info()%>%
 [^4]: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
 [^5]: https://github.com/qbic-pipelines/rnadeseq
 
+[^6]: https://github.com/nf-core/smrnaseq
+[^7]: https://github.com/OpenGene/fastp
+[^8]: https://github.com/friedlanderlab/mirtrace
diff --git a/assets/references.bibtex b/assets/references.bibtex
index fdf26cc2..92bccdc4 100644
--- a/assets/references.bibtex
+++ b/assets/references.bibtex
@@ -1,95 +1,95 @@
 @article{ewels2016multiqc,
-    title={MultiQC: summarize analysis results for multiple tools and samples in a single report},
-    author={Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and K{\"a}ller, Max},
-    journal={Bioinformatics},
-    volume={32},
-    number={19},
-    pages={3047--3048},
-    year={2016},
-    publisher={Oxford University Press}
+title={MultiQC: summarize analysis results for multiple tools and samples in a single report},
+author={Ewels, Philip and Magnusson, M{\aa}ns and Lundin, Sverker and K{\"a}ller, Max},
+journal={Bioinformatics},
+volume={32},
+number={19},
+pages={3047--3048},
+year={2016},
+publisher={Oxford University Press}
 }
 @article{kim2015hisat,
-    title={HISAT: a fast spliced aligner with low memory requirements},
-    author={Kim, Daehwan and Langmead, Ben and Salzberg, Steven L},
-    journal={Nature methods},
-    volume={12},
-    number={4},
-    pages={357},
-    year={2015},
-    publisher={Nature Publishing Group}
+title={HISAT: a fast spliced aligner with low memory requirements},
+author={Kim, Daehwan and Langmead, Ben and Salzberg, Steven L},
+journal={Nature methods},
+volume={12},
+number={4},
+pages={357},
+year={2015},
+publisher={Nature Publishing Group}
 }
 @article{wang2012rseqc,
-    title={RSeQC: quality control of RNA-seq experiments},
-    author={Wang, Liguo and Wang, Shengqin and Li, Wei},
-    journal={Bioinformatics},
-    volume={28},
-    number={16},
-    pages={2184--2185},
-    year={2012},
-    publisher={Oxford University Press}
+title={RSeQC: quality control of RNA-seq experiments},
+author={Wang, Liguo and Wang, Shengqin and Li, Wei},
+journal={Bioinformatics},
+volume={28},
+number={16},
+pages={2184--2185},
+year={2012},
+publisher={Oxford University Press}
 }
 @article{liao2014featurecounts,
-    title={featureCounts: an efficient general purpose program for assigning sequence reads to genomic features},
-    author={Liao, Yang and Smyth, Gordon K and Shi, Wei},
-    journal={Bioinformatics},
-    volume={30},
-    number={7},
-    pages={923--930},
-    year={2014}
+title={featureCounts: an efficient general purpose program for assigning sequence reads to genomic features},
+author={Liao, Yang and Smyth, Gordon K and Shi, Wei},
+journal={Bioinformatics},
+volume={30},
+number={7},
+pages={923--930},
+year={2014}
 }
 @article{love2014differential,
-    title={Differential analysis of count data--the DESeq2 package},
-    author={Love, Michael and Anders, Simon and Huber, Wolfgang},
-    journal={Genome Biol},
-    volume={15},
-    pages={550},
-    year={2014}
+title={Differential analysis of count data--the DESeq2 package},
+author={Love, Michael and Anders, Simon and Huber, Wolfgang},
+journal={Genome Biol},
+volume={15},
+pages={550},
+year={2014}
 }
 @article{Li2009,
-    author = {Li, Heng and Durbin, Richard},
-    title = {Fast and Accurate Short Read Alignment with Burrows--Wheeler Transform},
-    journal = {Bioinformatics},
-    issue_date = {July 2009},
-    volume = {25},
-    number = {14},
-    month = jul,
-    year = {2009},
-    issn = {1367-4803},
-    pages = {1754--1760},
-    numpages = {7},
-    url = {http://dx.doi.org/10.1093/bioinformatics/btp324},
-    doi = {10.1093/bioinformatics/btp324},
-    acmid = {1576130},
-    publisher = {Oxford University Press},
-    address = {Oxford, UK},
+author = {Li, Heng and Durbin, Richard},
+title = {Fast and Accurate Short Read Alignment with Burrows--Wheeler Transform},
+journal = {Bioinformatics},
+issue_date = {July 2009},
+volume = {25},
+number = {14},
+month = jul,
+year = {2009},
+issn = {1367-4803},
+pages = {1754--1760},
+numpages = {7},
+url = {http://dx.doi.org/10.1093/bioinformatics/btp324},
+doi = {10.1093/bioinformatics/btp324},
+acmid = {1576130},
+publisher = {Oxford University Press},
+address = {Oxford, UK},
 }
 @article{Lex2014,
-    doi = {10.1109/tvcg.2014.2346248},
-    url = {https://doi.org/10.1109/tvcg.2014.2346248},
-    year    = {2014},
-    month = {dec},
-    publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
-    volume = {20},
-    number = {12},
-    pages = {1983--1992},
-    author = {Alexander Lex and Nils Gehlenborg and Hendrik Strobelt and Romain Vuillemot and Hanspeter Pfister},
-    title = {{UpSet}: Visualization of Intersecting Sets},
-    journal = {{IEEE} Transactions on Visualization and Computer Graphics}
+doi = {10.1109/tvcg.2014.2346248},
+url = {https://doi.org/10.1109/tvcg.2014.2346248},
+year    = {2014},
+month = {dec},
+publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
+volume = {20},
+number = {12},
+pages = {1983--1992},
+author = {Alexander Lex and Nils Gehlenborg and Hendrik Strobelt and Romain Vuillemot and Hanspeter Pfister},
+title = {{UpSet}: Visualization of Intersecting Sets},
+journal = {{IEEE} Transactions on Visualization and Computer Graphics}
 }
 @article{Cingolani2012,
-    title={Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift},
-    author={Cingolani, P. and Patel, V.M. and Coon, M. and Nguyen, T. and Land, S.J. and Ruden, D.M. and Lu, X.},
-    journal={Frontiers in Genetics},
-    volume={3},
-    year={2012},
-    publisher={Frontiers Media SA}
+title={Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift},
+author={Cingolani, P. and Patel, V.M. and Coon, M. and Nguyen, T. and Land, S.J. and Ruden, D.M. and Lu, X.},
+journal={Frontiers in Genetics},
+volume={3},
+year={2012},
+publisher={Frontiers Media SA}
 }
 @article{Garrison2012,
-    title={Haplotype-based variant detection from short-read sequencing},
-    author={Garrison, E. and Marth, G.},
-    journal={arXiv:1207.3907},
-    publisher={[q-bio.GN]},
-    year={2012}
+title={Haplotype-based variant detection from short-read sequencing},
+author={Garrison, E. and Marth, G.},
+journal={arXiv:1207.3907},
+publisher={[q-bio.GN]},
+year={2012}
 }
 @article{Dobin2013,
 author = {Dobin, A. and Davis, C.A. and Schlesinger, F. and Drenkow, J. and Zaleski, C. and Jha, S. and Batut, P. and Chaisson, M. and Gingeras, T.R.},
@@ -168,51 +168,109 @@ title="dupRadar: a Bioconductor package for the assessment of PCR artifacts in R
 journal="BMC Bioinformatics",
 }
 @article{krueger2012trim,
-    title={Trim Galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries},
-    author={Krueger, F},
-    journal={URL http://www.bioinformatics.babraham.ac.uk/projects/trim\_galore/},
-    year={2012}
+title={Trim Galore: a wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries},
+author={Krueger, F},
+journal={URL http://www.bioinformatics.babraham.ac.uk/projects/trim\_galore/},
+year={2012}
 }
 @article{sayols2016dupradar,
-    title={dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data},
-    author={Sayols, Sergi and Scherzinger, Denise and Klein, Holger},
-    journal={BMC bioinformatics},
-    volume={17},
-    number={1},
-    pages={428},
-    year={2016},
-    publisher={BioMed Central}
+title={dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data},
+author={Sayols, Sergi and Scherzinger, Denise and Klein, Holger},
+journal={BMC bioinformatics},
+volume={17},
+number={1},
+pages={428},
+year={2016},
+publisher={BioMed Central}
 }
 @misc{andrews2010fastqc,
-    title={FastQC: a quality control tool for high throughput sequence data},
-    author={Andrews, Simon and others},
-    year={2010}
+title={FastQC: a quality control tool for high throughput sequence data},
+author={Andrews, Simon and others},
+year={2010}
 }
 @Book{ggplot,
-    author = {Hadley Wickham},
-    title = {ggplot2: Elegant Graphics for Data Analysis},
-    publisher = {Springer-Verlag New York},
-    year = {2016},
-    isbn = {978-3-319-24277-4},
-    url = {http://ggplot2.org},
+author = {Hadley Wickham},
+title = {ggplot2: Elegant Graphics for Data Analysis},
+publisher = {Springer-Verlag New York},
+year = {2016},
+isbn = {978-3-319-24277-4},
+url = {http://ggplot2.org},
 }
 @article{anders2012detecting,
-    title={Detecting differential usage of exons from RNA-seq data},
-    author={Anders, Simon and Reyes, Alejandro and Huber, Wolfgang},
-    journal={Genome research},
-    volume={22},
-    number={10},
-    pages={2008--2017},
-    year={2012},
-    publisher={Cold Spring Harbor Lab}
+title={Detecting differential usage of exons from RNA-seq data},
+author={Anders, Simon and Reyes, Alejandro and Huber, Wolfgang},
+journal={Genome research},
+volume={22},
+number={10},
+pages={2008--2017},
+year={2012},
+publisher={Cold Spring Harbor Lab}
 }
 @article{ewels2020nf,
-    title={The nf-core framework for community-curated bioinformatics pipelines},
-    author={Ewels, Philip A and Peltzer, Alexander and Fillinger, Sven and Patel, Harshil and Alneberg, Johannes and Wilm, Andreas and Garcia, Maxime Ulysse and Di Tommaso, Paolo and Nahnsen, Sven},
-    journal={Nature biotechnology},
-    volume={38},
-    number={3},
-    pages={276--278},
-    year={2020},
-    publisher={Nature Publishing Group}
+title={The nf-core framework for community-curated bioinformatics pipelines},
+author={Ewels, Philip A and Peltzer, Alexander and Fillinger, Sven and Patel, Harshil and Alneberg, Johannes and Wilm, Andreas and Garcia, Maxime Ulysse and Di Tommaso, Paolo and Nahnsen, Sven},
+journal={Nature biotechnology},
+volume={38},
+number={3},
+pages={276--278},
+year={2020},
+publisher={Nature Publishing Group}
+}
+@article{kang2018mirtrace,
+title={miRTrace reveals the organismal origins of microRNA sequencing data},
+author={Kang, Wenjing and Eldfjell, Yrin and Fromm, Bastian and Estivill, Xavier and Biryukova, Inna and Friedl{\"a}nder, Marc R},
+journal={Genome biology},
+volume={19},
+number={1},
+pages={1--15},
+year={2018},
+publisher={BioMed Central}
+}
+@article{langmead2009ultrafast,
+title={Ultrafast and memory-efficient alignment of short DNA sequences to the human genome},
+author={Langmead, Ben and Trapnell, Cole and Pop, Mihai and Salzberg, Steven L},
+journal={Genome biology},
+volume={10},
+number={3},
+pages={1--10},
+year={2009},
+publisher={BioMed Central}
+}
+@article{chen2018fastp,
+title={fastp: an ultra-fast all-in-one FASTQ preprocessor},
+author={Chen, Shifu and Zhou, Yanqing and Chen, Yaru and Gu, Jia},
+journal={Bioinformatics},
+volume={34},
+number={17},
+pages={i884--i890},
+year={2018},
+publisher={Oxford University Press}
+}
+@article{chen2023ultrafast,
+title={Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp},
+author={Chen, Shifu},
+journal={iMeta},
+pages={e107},
+year={2023},
+publisher={Wiley Online Library}
+}
+@article{li2009sequence,
+title={The sequence alignment/map format and SAMtools},
+author={Li, Heng and Handsaker, Bob and Wysoker, Alec and Fennell, Tim and Ruan, Jue and Homer, Nils and Marth, Gabor and Abecasis, Goncalo and Durbin, Richard and 1000 Genome Project Data Processing Subgroup},
+journal={bioinformatics},
+volume={25},
+number={16},
+pages={2078--2079},
+year={2009},
+publisher={Oxford University Press}
+}
+@article{li2011statistical,
+title={A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data},
+author={Li, Heng},
+journal={Bioinformatics},
+volume={27},
+number={21},
+pages={2987--2993},
+year={2011},
+publisher={Oxford University Press}
 }
diff --git a/conf/test_smrnaseq.config b/conf/test_smrnaseq.config
new file mode 100644
index 00000000..797fa332
--- /dev/null
+++ b/conf/test_smrnaseq.config
@@ -0,0 +1,32 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for running tests
+ * -------------------------------------------------
+ * Defines bundled input files and everything required
+ * to run a fast and simple test. Use as follows:
+ *   nextflow run qbic-pipelines/rnadeseq -profile test_smrnaseq
+ */
+
+params {
+    config_profile_name = 'Test smrnaseq'
+    config_profile_description = 'Minimal test dataset to check pipeline function'
+    // Limit resources so that this can run on Travis
+    max_cpus = 2
+    max_memory = 6.GB
+    max_time = 48.h
+    // Input data
+    input = 'testdata/smrnaseq/samplesheet.tsv'
+    gene_counts = 'testdata/smrnaseq/counts'
+    model = 'testdata/smrnaseq/design.txt'
+    logFC_threshold = 1
+    project_summary = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/summary.tsv'
+    software_versions = 'https://raw.githubusercontent.com/qbic-pipelines/rnadeseq/dev/testdata/software_versions_smrnaseq.yml'
+    genelist = 'testdata/smrnaseq/requested_genes.txt'
+    input_type = 'smrnaseq'
+    run_pathway_analysis = true
+    genome = 'GRCh37'
+    batch_effect = true
+    set_background = false // This is solely to get some enriched pathways so that the github tests also check the pathway analysis output
+    // species_library     = "org.Hs.eg.db"
+    // organism    = "hsapiens"
+}
diff --git a/docs/output.md b/docs/output.md
index bdc278d0..3c30fd18 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -27,8 +27,9 @@ This directory contains the zipped results. When unzipping them, the following s
   - `linear_model.txt`: linear model used for DE analysis.
   - `gene_list.txt`: provided list of interesting genes (if provided).
   - `star_[rsem/salmon]_files.txt`: list of counts files that were provided as input (only if `--input_type` is `rsem` or `salmon`).
+  - `smrnaseq_files.txt`: list of counts files that were provided as input (only if `--input_type` is `smrnaseq`).
 - `gene_counts_tables/`
-  - `raw_gene_counts.txt`: raw gene counts table from the nf-core/rnaseq pipeline and used for the differential gene expression analysis (only if `--input_type` is `featurecounts`).
+  - `raw_gene_counts.txt`: raw gene counts table from the nf-core/rnaseq pipeline and used for the differential gene expression analysis (only if `--input_type` is `featurecounts` or `smrnaseq`; in the second case, will internally build a counts table from the input files, taking the third column of each .sorted.idxstats file (second column if counting rownames) and combining all values from both hairpin and non-hairpin mature files into one table).
   - `rlog_transformed_gene_counts.tsv`: normalized gene counts with the "regularized logarithm" approach. This normalization is used prior to PCA analysis and heatmap plotting of the gene counts (only when rlog transformation is used).
   - `vst_transformed_gene_counts.tsv`: normalized gene counts with the "variance stabilizing" transformation (only when vst transformation is used).
   - `sizeFactor_libraries.tsv`: size factors for each sample.
@@ -47,7 +48,7 @@ Pathway analysis with [gProfileR](https://biit.cs.ut.ee/gprofiler/gost) R packag
 
 **Output directory: `results/pathway_analysis/`**
 
-This directory contains the zipped pathway analysis results (`gProfileR.zip`). When unzipping them, a subfolder for each contrast used for the differential gene expression analysis is found. Inside each contrast folder, there is the following output:
+If pathway analysis was run, this directory contains the zipped pathway analysis results (`gProfileR.zip`). When unzipping them, a subfolder for each contrast used for the differential gene expression analysis is found. Inside each contrast folder, there is the following output:
 
 - `*_gost_pathway_venn_diagram.pdf/png`
   - Venn diagrams showing the numbers of enriched pathways when using a background gene list vs when not using a bg list.
@@ -66,8 +67,6 @@ QBiC report for RNAseq analysis.
 
 In this directory the zipped report is contained. This file is ready for upload to the project in the QBiC portal. Once unzipped, this directory contains:
 
-<!-- Here also remove the QC stuff? But then, nothing remains, right? -->
-
 - `Report.html`
   - QBiC report describing the RNAseq results.
 - `DESeq2/`
@@ -75,6 +74,6 @@ In this directory the zipped report is contained. This file is ready for upload
 - `QC/`
   - Quality control results. Contains:
   - `fastqc.zip`: zipped fastqc results for each sample.
-  - `multiqc_data`: data from the multiQC process of the RNAseq pipeline which is incorporated into the report.
-  - `multiqc_plots`: plots from the multiQC process of the RNAseq pipeline which are incorporated into the report.
-  - `qc_summary.tsv`: summary of the multiQC process in a table format.
+  - `multiqc_data`: If multiQC input was provided: data from the multiQC process of the RNAseq pipeline which is incorporated into the report.
+  - `multiqc_plots`: If multiQC input was provided: plots from the multiQC process of the RNAseq pipeline which are incorporated into the report.
+  - `qc_summary.tsv`: If multiQC input was provided: summary of the multiQC process in a table format.
diff --git a/docs/usage.md b/docs/usage.md
index 13587b1f..2f6719e4 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -82,7 +82,7 @@ NXF_OPTS='-Xms1g -Xmx4g'
 
 ## Pre-requisites
 
-The `qbic-pipelines/rnadeseq` pipeline relies on the output from the `nf-core/rnaseq` pipeline. To be able to match the results of the `nf-core/rnaseq` pipeline with the metadata samplesheet containing the experimental design for the differential expression analysis, **the filenames of the fastq files used as input to the `qbic-pipelines/rnadeseq` pipeline, need to start with the corresponding QBiC codes!**. _E.g. QBICKXXXXX_original_file_name.fastq_. Once the filenames are corrected if necessary, you can run the `qbic-pipelines/rnadeseq` pipeline as usual.
+The `qbic-pipelines/rnadeseq` pipeline relies on the output from the `nf-core/rnaseq` pipeline or the `nf-core/smrnaseq` pipeline. To be able to match the results of the initial pipeline with the metadata samplesheet containing the experimental design for the differential expression analysis, **the filenames of the fastq files used as input to the `qbic-pipelines/rnadeseq` pipeline need to start with the corresponding QBiC codes!**. _E.g. QBICKXXXXX_original_file_name.fastq_. Once the filenames are corrected if necessary, you can run the `qbic-pipelines/rnadeseq` pipeline as usual.
 
 ## Running the pipeline
 
@@ -218,6 +218,36 @@ QDESQ083AC      Sample3 K562
 QDESQ084AK      Sample4 K562
 ```
 
+- OR a folder containing files with smrnaseq output (folder/sampleXXX_mature_hairpin.sorted.idxstats, folder/sampleXXX_mature_sorted.idxstats).
+  For smrnaseq, the --input_type parameter must be set to 'smrnaseq'.
+  For example:
+
+```bash
+--gene_counts 'path/to/smrnaseq_folder' --metadata 'path/to/smrnaseq_metadata.tsv'
+
+tree testdata/smrnaseq/counts/
+testdata/smrnaseq/counts/
+├── Clone1_NN1_mature.sorted.idxstats
+├── Clone1_NN1_mature_hairpin.sorted.idxstats
+├── Clone1_NN3_mature.sorted.idxstats
+├── Clone1_NN3_mature_hairpin.sorted.idxstats
+├── Clone9_NN1_mature.sorted.idxstats
+├── Clone9_NN1_mature_hairpin.sorted.idxstats
+.
+.
+.
+
+head 'path/to/smrnaseq_metadata.tsv'
+```
+
+```tsv
+QBiC Code       Secondary Name  Condition: cellline
+QDESQ081AU      Sample1 GM12878
+QDESQ082A4      Sample2 GM12878
+QDESQ083AC      Sample3 K562
+QDESQ084AK      Sample4 K562
+```
+
 ### `--input`
 
 Metadata table/samplesheet (TSV) is the "Sample_preparations_sheet.tsv" that can be directly downloaded from the qPortal --> Browser. Rows are samples and columns contain sample grouping. Important columns are:
@@ -344,7 +374,7 @@ Set this flag to run pathway analysis, otherwise, this step will be skipped.
 
 ### `--input_type`
 
-This tells the pipeline which type of input dataset is provided. Must be one of 'featurecounts', 'rsem', 'salmon', default: featurecounts.
+This tells the pipeline which type of input dataset is provided. Must be one of 'featurecounts', 'rsem', 'salmon', 'smrnaseq', default: featurecounts.
 
 ### `--multiqc`
 
@@ -393,7 +423,7 @@ Which genome to use for analysis, e.g. GRCh37; see `/conf/igenomes.config` for w
 
 ### `--gtf`
 
-GTF file to be used for DESeq if input is rsem or salmon, not necessary for featurecounts.
+GTF file to be used for DESeq if input is rsem or salmon, not necessary for featurecounts or smrnaseq.
 
 ### `--organism`
 
diff --git a/nextflow.config b/nextflow.config
index fd1595d6..866a45e4 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -198,6 +198,7 @@ profiles {
     test_contrast_list { includeConfig 'conf/test_contrast_list.config' }
     test_relevel { includeConfig 'conf/test_relevel.config' }
     test_use_vst { includeConfig 'conf/test_use_vst.config' }
+    test_smrnaseq { includeConfig 'conf/test_smrnaseq.config' }
     test_star_salmon { includeConfig 'conf/test_star_salmon.config' }
     test_star_rsem { includeConfig 'conf/test_star_rsem.config' }
     test_batcheffect { includeConfig 'conf/test_batcheffect.config' }
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 3aec2e6a..e992d9cd 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -13,11 +13,11 @@
                 "input_type": {
                     "type": "string",
                     "default": "featurecounts",
-                    "description": "Which type of input is provided, one of featurecounts, rsem, salmon"
+                    "description": "Which type of input is provided, one of featurecounts, rsem, salmon, smrnaseq."
                 },
                 "gene_counts": {
                     "type": "string",
-                    "description": "If input_type = featurecounts: Raw count table (TSV). Columns are samples and rows are genes. 1st column Ensembl_ID, 2nd column gene_name. If input_type = rsem or input_type = salmon: Path to rsem/salmon output folder."
+                    "description": "If input_type = featurecounts: Raw count table (TSV). Columns are samples and rows are genes. 1st column Ensembl_ID, 2nd column gene_name. If input_type = rsem or input_type = salmon: Path to rsem/salmon output folder. If input_type = smrnaseq: Path to smrnaseq output folder containing hairpin and non-hairpin mature .sorted.idxstats files."
                 },
                 "input": {
                     "type": "string",
diff --git a/testdata/smrnaseq/counts/Clone1_NN1_mature.sorted.idxstats b/testdata/smrnaseq/counts/Clone1_NN1_mature.sorted.idxstats
new file mode 100644
index 00000000..8ccd1462
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone1_NN1_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
+hsa-let-7a-5p	22	0	0
+hsa-let-7a-3p	21	0	0
+hsa-let-7a-2-3p	22	0	0
+hsa-let-7b-5p	22	0	0
+hsa-let-7b-3p	22	0	0
+hsa-let-7c-5p	22	0	0
+hsa-let-7c-3p	22	0	0
+hsa-let-7d-5p	22	0	0
+hsa-let-7d-3p	22	0	0
+hsa-let-7e-5p	22	0	0
+hsa-let-7e-3p	22	0	0
+hsa-let-7f-5p	22	0	0
+hsa-let-7f-1-3p	22	0	0
+hsa-let-7f-2-3p	22	0	0
+hsa-miR-15a-5p	22	0	0
+hsa-miR-15a-3p	22	0	0
+hsa-miR-16-5p	22	0	0
+hsa-miR-16-1-3p	22	0	0
+hsa-miR-17-5p	23	0	0
+hsa-miR-17-3p	22	0	0
+hsa-miR-18a-5p	23	0	0
+hsa-miR-18a-3p	23	0	0
+hsa-miR-19a-5p	22	0	0
+hsa-miR-19a-3p	23	0	0
+hsa-miR-19b-1-5p	23	0	0
+hsa-miR-19b-3p	23	0	0
+hsa-miR-19b-2-5p	22	0	0
+hsa-miR-20a-5p	23	0	0
+hsa-miR-20a-3p	22	0	0
+hsa-miR-21-5p	22	0	0
+hsa-miR-21-3p	21	0	0
+hsa-miR-22-5p	22	0	0
+hsa-miR-22-3p	22	0	0
+hsa-miR-23a-5p	22	0	0
+hsa-miR-23a-3p	21	0	0
+hsa-miR-24-1-5p	22	0	0
+hsa-miR-24-3p	22	0	0
+hsa-miR-24-2-5p	22	0	0
+hsa-miR-25-5p	21	0	0
+hsa-miR-25-3p	22	0	0
+hsa-miR-26a-5p	22	0	0
+hsa-miR-26a-1-3p	22	0	0
+hsa-miR-26b-5p	21	0	0
+hsa-miR-26b-3p	22	0	0
+hsa-miR-27a-5p	22	0	0
+hsa-miR-27a-3p	21	0	0
+hsa-miR-28-5p	22	0	0
+hsa-miR-28-3p	22	0	0
+hsa-miR-29a-5p	22	0	0
+hsa-miR-29a-3p	22	0	0
+hsa-miR-30a-5p	22	0	0
+hsa-miR-30a-3p	22	0	0
+hsa-miR-31-5p	21	0	0
+hsa-miR-31-3p	22	0	0
+hsa-miR-32-5p	22	0	0
+hsa-miR-32-3p	22	0	0
+hsa-miR-33a-5p	21	0	0
+hsa-miR-33a-3p	22	0	0
+hsa-miR-92a-1-5p	23	0	0
+hsa-miR-92a-3p	22	0	0
+hsa-miR-92a-2-5p	22	0	0
+hsa-miR-93-5p	23	0	0
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+hsa-miR-6834-3p	20	0	0
+hsa-miR-6835-5p	22	0	0
+hsa-miR-6835-3p	23	0	0
+hsa-miR-6780b-5p	23	0	0
+hsa-miR-6780b-3p	21	0	0
+hsa-miR-6836-5p	22	0	0
+hsa-miR-6836-3p	21	0	0
+hsa-miR-6837-5p	21	0	0
+hsa-miR-6837-3p	23	0	0
+hsa-miR-6838-5p	22	0	0
+hsa-miR-6838-3p	20	0	0
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+hsa-miR-6840-5p	24	0	0
+hsa-miR-6840-3p	22	0	0
+hsa-miR-6841-5p	22	0	0
+hsa-miR-6841-3p	21	0	0
+hsa-miR-6842-5p	22	0	0
+hsa-miR-6842-3p	22	0	0
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+hsa-miR-6844	21	0	0
+hsa-miR-6845-5p	19	0	0
+hsa-miR-6845-3p	21	0	0
+hsa-miR-6846-5p	22	0	0
+hsa-miR-6846-3p	21	0	0
+hsa-miR-6847-5p	23	0	0
+hsa-miR-6847-3p	22	0	0
+hsa-miR-6848-5p	23	0	0
+hsa-miR-6848-3p	19	0	0
+hsa-miR-6849-5p	23	0	0
+hsa-miR-6849-3p	22	0	0
+hsa-miR-6850-5p	22	0	0
+hsa-miR-6850-3p	20	0	0
+hsa-miR-6851-5p	23	0	0
+hsa-miR-6851-3p	21	0	0
+hsa-miR-6852-5p	21	0	0
+hsa-miR-6852-3p	17	0	0
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+hsa-miR-6853-3p	22	0	0
+hsa-miR-6854-5p	24	0	0
+hsa-miR-6854-3p	21	0	0
+hsa-miR-6855-5p	25	0	0
+hsa-miR-6855-3p	22	0	0
+hsa-miR-6856-5p	24	0	0
+hsa-miR-6856-3p	22	0	0
+hsa-miR-6857-5p	22	0	0
+hsa-miR-6857-3p	21	0	0
+hsa-miR-6858-5p	22	0	0
+hsa-miR-6858-3p	22	0	0
+hsa-miR-6859-5p	23	0	0
+hsa-miR-6859-3p	23	0	0
+hsa-miR-6769b-5p	23	0	0
+hsa-miR-6769b-3p	21	0	0
+hsa-miR-6860	22	0	0
+hsa-miR-6861-5p	22	0	0
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+hsa-miR-6862-3p	24	0	0
+hsa-miR-6863	23	0	0
+hsa-miR-6864-5p	24	0	0
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+hsa-miR-6865-5p	23	0	0
+hsa-miR-6865-3p	21	0	0
+hsa-miR-6866-5p	23	0	0
+hsa-miR-6866-3p	22	0	0
+hsa-miR-6867-5p	23	0	0
+hsa-miR-6867-3p	21	0	0
+hsa-miR-6868-5p	22	0	0
+hsa-miR-6868-3p	21	0	0
+hsa-miR-6869-5p	22	0	0
+hsa-miR-6869-3p	21	0	0
+hsa-miR-6870-5p	19	0	0
+hsa-miR-6870-3p	22	0	0
+hsa-miR-6871-5p	22	0	0
+hsa-miR-6871-3p	22	0	0
+hsa-miR-6872-5p	20	0	0
+hsa-miR-6872-3p	21	0	0
+hsa-miR-6873-5p	22	0	0
+hsa-miR-6873-3p	23	0	0
+hsa-miR-6874-5p	23	0	0
+hsa-miR-6874-3p	23	0	0
+hsa-miR-6875-5p	21	0	0
+hsa-miR-6875-3p	22	0	0
+hsa-miR-6876-5p	22	0	0
+hsa-miR-6876-3p	24	0	0
+hsa-miR-6877-5p	22	0	0
+hsa-miR-6877-3p	21	0	0
+hsa-miR-6878-5p	23	0	0
+hsa-miR-6878-3p	21	0	0
+hsa-miR-6879-5p	22	0	0
+hsa-miR-6879-3p	21	0	0
+hsa-miR-6880-5p	22	0	0
+hsa-miR-6880-3p	21	0	0
+hsa-miR-6881-5p	22	0	0
+hsa-miR-6881-3p	22	0	0
+hsa-miR-6882-5p	22	0	0
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+hsa-miR-6883-3p	22	0	0
+hsa-miR-6884-5p	22	0	0
+hsa-miR-6884-3p	23	0	0
+hsa-miR-6885-5p	25	0	0
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+hsa-miR-6886-5p	21	0	0
+hsa-miR-6886-3p	21	0	0
+hsa-miR-6887-5p	23	0	0
+hsa-miR-6887-3p	21	0	0
+hsa-miR-6888-5p	20	0	0
+hsa-miR-6888-3p	21	0	0
+hsa-miR-6889-5p	23	0	0
+hsa-miR-6889-3p	20	0	0
+hsa-miR-6890-5p	21	0	0
+hsa-miR-6890-3p	20	0	0
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+hsa-miR-9500	19	0	0
+hsa-miR-548bb-5p	22	0	0
+hsa-miR-548bb-3p	22	0	0
+*	0	0	2193613
diff --git a/testdata/smrnaseq/counts/Clone1_NN1_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Clone1_NN1_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..5e20365d
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone1_NN1_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
+hsa-let-7a-1	80	1339	0
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+*	0	0	2167800
diff --git a/testdata/smrnaseq/counts/Clone1_NN3_mature.sorted.idxstats b/testdata/smrnaseq/counts/Clone1_NN3_mature.sorted.idxstats
new file mode 100644
index 00000000..095d2a32
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone1_NN3_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
+hsa-let-7a-5p	22	0	0
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diff --git a/testdata/smrnaseq/counts/Clone1_NN3_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Clone1_NN3_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..399b6528
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone1_NN3_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
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diff --git a/testdata/smrnaseq/counts/Clone9_NN1_mature.sorted.idxstats b/testdata/smrnaseq/counts/Clone9_NN1_mature.sorted.idxstats
new file mode 100644
index 00000000..022f65f0
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone9_NN1_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
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+hsa-miR-6852-5p	21	0	0
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+hsa-miR-6855-5p	25	0	0
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+hsa-miR-6857-5p	22	0	0
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+hsa-miR-6858-5p	22	0	0
+hsa-miR-6858-3p	22	0	0
+hsa-miR-6859-5p	23	0	0
+hsa-miR-6859-3p	23	0	0
+hsa-miR-6769b-5p	23	0	0
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+hsa-miR-6868-3p	21	0	0
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+hsa-miR-548bb-5p	22	0	0
+hsa-miR-548bb-3p	22	0	0
+*	0	0	2495471
diff --git a/testdata/smrnaseq/counts/Clone9_NN1_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Clone9_NN1_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..f296b34f
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone9_NN1_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
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+hsa-mir-7110	86	0	0
+hsa-mir-7111	72	0	0
+hsa-mir-7112	65	0	0
+hsa-mir-7113	59	0	0
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+hsa-mir-6511b-2	71	1	0
+hsa-mir-3690-2	75	0	0
+hsa-mir-6089-2	64	0	0
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+hsa-mir-7158	71	0	0
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+hsa-mir-7160	52	0	0
+hsa-mir-486-2	64	0	0
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+hsa-mir-7515	67	0	0
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+hsa-mir-7641-2	53	447	0
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+hsa-mir-7705	57	0	0
+hsa-mir-7706	67	0	0
+hsa-mir-7843	79	0	0
+hsa-mir-4433b	102	0	0
+hsa-mir-1273h	116	0	0
+hsa-mir-6516	81	0	0
+hsa-mir-7844	122	0	0
+hsa-mir-7845	99	0	0
+hsa-mir-7846	96	0	0
+hsa-mir-7847	103	0	0
+hsa-mir-7848	101	0	0
+hsa-mir-7849	106	0	0
+hsa-mir-7850	79	0	0
+hsa-mir-7851	160	1	0
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+hsa-mir-7853	132	0	0
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+hsa-mir-5701-3	82	0	0
+*	0	0	2472791
diff --git a/testdata/smrnaseq/counts/Clone9_NN2_mature.sorted.idxstats b/testdata/smrnaseq/counts/Clone9_NN2_mature.sorted.idxstats
new file mode 100644
index 00000000..71022913
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone9_NN2_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
+hsa-let-7a-5p	22	4	0
+hsa-let-7a-3p	21	0	0
+hsa-let-7a-2-3p	22	0	0
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+hsa-let-7b-3p	22	0	0
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+hsa-let-7c-3p	22	0	0
+hsa-let-7d-5p	22	0	0
+hsa-let-7d-3p	22	0	0
+hsa-let-7e-5p	22	0	0
+hsa-let-7e-3p	22	0	0
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+hsa-let-7f-1-3p	22	0	0
+hsa-let-7f-2-3p	22	0	0
+hsa-miR-15a-5p	22	0	0
+hsa-miR-15a-3p	22	0	0
+hsa-miR-16-5p	22	0	0
+hsa-miR-16-1-3p	22	0	0
+hsa-miR-17-5p	23	0	0
+hsa-miR-17-3p	22	0	0
+hsa-miR-18a-5p	23	0	0
+hsa-miR-18a-3p	23	0	0
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+hsa-miR-19a-3p	23	0	0
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+hsa-miR-19b-2-5p	22	0	0
+hsa-miR-20a-5p	23	0	0
+hsa-miR-20a-3p	22	0	0
+hsa-miR-21-5p	22	0	0
+hsa-miR-21-3p	21	0	0
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+hsa-miR-22-3p	22	0	0
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+hsa-miR-24-1-5p	22	0	0
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+hsa-let-7g-5p	22	0	0
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+*	0	0	1922831
diff --git a/testdata/smrnaseq/counts/Clone9_NN2_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Clone9_NN2_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..7a7ce005
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone9_NN2_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
+hsa-let-7a-1	80	562	0
+hsa-let-7a-2	72	705	0
+hsa-let-7a-3	74	10	0
+hsa-let-7b	83	478	0
+hsa-let-7c	84	564	0
+hsa-let-7d	87	32	0
+hsa-let-7e	79	79	0
+hsa-let-7f-1	87	826	0
+hsa-let-7f-2	83	135	0
+hsa-mir-15a	83	0	0
+hsa-mir-16-1	89	14	0
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diff --git a/testdata/smrnaseq/counts/Clone9_NN3_mature.sorted.idxstats b/testdata/smrnaseq/counts/Clone9_NN3_mature.sorted.idxstats
new file mode 100644
index 00000000..3d15982c
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone9_NN3_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
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+hsa-miR-6864-5p	24	0	0
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+hsa-miR-6865-3p	21	0	0
+hsa-miR-6866-5p	23	0	0
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+hsa-miR-6867-5p	23	0	0
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+hsa-miR-6868-5p	22	0	0
+hsa-miR-6868-3p	21	0	0
+hsa-miR-6869-5p	22	0	0
+hsa-miR-6869-3p	21	0	0
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+hsa-miR-6872-3p	21	0	0
+hsa-miR-6873-5p	22	0	0
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+hsa-miR-6874-5p	23	0	0
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+hsa-miR-6875-5p	21	0	0
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+hsa-miR-9500	19	0	0
+hsa-miR-548bb-5p	22	0	0
+hsa-miR-548bb-3p	22	0	0
+*	0	0	1487807
diff --git a/testdata/smrnaseq/counts/Clone9_NN3_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Clone9_NN3_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..37948f60
--- /dev/null
+++ b/testdata/smrnaseq/counts/Clone9_NN3_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
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+hsa-mir-7706	67	0	0
+hsa-mir-7843	79	0	0
+hsa-mir-4433b	102	0	0
+hsa-mir-1273h	116	0	0
+hsa-mir-6516	81	0	0
+hsa-mir-7844	122	0	0
+hsa-mir-7845	99	0	0
+hsa-mir-7846	96	0	0
+hsa-mir-7847	103	0	0
+hsa-mir-7848	101	0	0
+hsa-mir-7849	106	0	0
+hsa-mir-7850	79	0	0
+hsa-mir-7851	160	1	0
+hsa-mir-7852	82	0	0
+hsa-mir-7853	132	0	0
+hsa-mir-7854	65	0	0
+hsa-mir-7855	61	0	0
+hsa-mir-7856	56	0	0
+hsa-mir-548ba	56	0	0
+hsa-mir-7973-1	76	0	0
+hsa-mir-7973-2	76	0	0
+hsa-mir-7974	79	0	0
+hsa-mir-7975	68	0	0
+hsa-mir-7976	66	0	0
+hsa-mir-7977	49	0	0
+hsa-mir-7978	59	0	0
+hsa-mir-8052	69	0	0
+hsa-mir-8053	75	0	0
+hsa-mir-8054	86	0	0
+hsa-mir-8055	97	0	0
+hsa-mir-8056	82	0	0
+hsa-mir-8057	69	0	0
+hsa-mir-8058	89	0	0
+hsa-mir-8059	81	0	0
+hsa-mir-8060	76	0	0
+hsa-mir-8061	75	0	0
+hsa-mir-8062	85	0	0
+hsa-mir-8063	81	0	0
+hsa-mir-8064	90	0	0
+hsa-mir-8065	100	0	0
+hsa-mir-8066	78	0	0
+hsa-mir-8067	77	0	0
+hsa-mir-8068	68	0	0
+hsa-mir-8069-1	86	0	0
+hsa-mir-8070	88	0	0
+hsa-mir-8071-1	65	0	0
+hsa-mir-8072	80	1	0
+hsa-mir-8073	72	0	0
+hsa-mir-8074	81	0	0
+hsa-mir-8075	80	0	0
+hsa-mir-8076	83	0	0
+hsa-mir-8077	75	0	0
+hsa-mir-8078	84	0	0
+hsa-mir-8079	72	0	0
+hsa-mir-8080	89	0	0
+hsa-mir-8081	95	0	0
+hsa-mir-8082	81	0	0
+hsa-mir-8083	89	0	0
+hsa-mir-8084	89	0	0
+hsa-mir-8085	65	0	0
+hsa-mir-8086	93	0	0
+hsa-mir-8087	78	0	0
+hsa-mir-8088	86	0	0
+hsa-mir-8089	82	0	0
+hsa-mir-6862-2	70	0	0
+hsa-mir-8071-2	65	0	0
+hsa-mir-6770-2	60	0	0
+hsa-mir-6770-3	60	0	0
+hsa-mir-6859-2	68	0	0
+hsa-mir-6859-3	68	0	0
+hsa-mir-8485	91	0	0
+hsa-mir-9500	65	0	0
+hsa-mir-548bb	66	0	0
+hsa-mir-3179-4	84	0	0
+hsa-mir-1244-4	85	0	0
+hsa-mir-3648-2	180	2	0
+hsa-mir-3670-3	65	0	0
+hsa-mir-3670-4	65	0	0
+hsa-mir-3687-2	61	0	0
+hsa-mir-6724-2	92	0	0
+hsa-mir-6724-3	92	0	0
+hsa-mir-6724-4	92	0	0
+hsa-mir-8069-2	86	0	0
+hsa-mir-941-5	72	0	0
+hsa-mir-6859-4	68	0	0
+hsa-mir-5701-3	82	0	0
+*	0	0	1480981
diff --git a/testdata/smrnaseq/counts/Control_N1_mature.sorted.idxstats b/testdata/smrnaseq/counts/Control_N1_mature.sorted.idxstats
new file mode 100644
index 00000000..c6c73776
--- /dev/null
+++ b/testdata/smrnaseq/counts/Control_N1_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
+hsa-let-7a-5p	22	0	0
+hsa-let-7a-3p	21	0	0
+hsa-let-7a-2-3p	22	0	0
+hsa-let-7b-5p	22	0	0
+hsa-let-7b-3p	22	0	0
+hsa-let-7c-5p	22	0	0
+hsa-let-7c-3p	22	0	0
+hsa-let-7d-5p	22	0	0
+hsa-let-7d-3p	22	0	0
+hsa-let-7e-5p	22	0	0
+hsa-let-7e-3p	22	0	0
+hsa-let-7f-5p	22	0	0
+hsa-let-7f-1-3p	22	0	0
+hsa-let-7f-2-3p	22	0	0
+hsa-miR-15a-5p	22	0	0
+hsa-miR-15a-3p	22	0	0
+hsa-miR-16-5p	22	0	0
+hsa-miR-16-1-3p	22	0	0
+hsa-miR-17-5p	23	0	0
+hsa-miR-17-3p	22	0	0
+hsa-miR-18a-5p	23	0	0
+hsa-miR-18a-3p	23	0	0
+hsa-miR-19a-5p	22	0	0
+hsa-miR-19a-3p	23	0	0
+hsa-miR-19b-1-5p	23	0	0
+hsa-miR-19b-3p	23	0	0
+hsa-miR-19b-2-5p	22	0	0
+hsa-miR-20a-5p	23	0	0
+hsa-miR-20a-3p	22	0	0
+hsa-miR-21-5p	22	0	0
+hsa-miR-21-3p	21	0	0
+hsa-miR-22-5p	22	0	0
+hsa-miR-22-3p	22	0	0
+hsa-miR-23a-5p	22	0	0
+hsa-miR-23a-3p	21	0	0
+hsa-miR-24-1-5p	22	0	0
+hsa-miR-24-3p	22	0	0
+hsa-miR-24-2-5p	22	0	0
+hsa-miR-25-5p	21	0	0
+hsa-miR-25-3p	22	0	0
+hsa-miR-26a-5p	22	0	0
+hsa-miR-26a-1-3p	22	0	0
+hsa-miR-26b-5p	21	0	0
+hsa-miR-26b-3p	22	0	0
+hsa-miR-27a-5p	22	0	0
+hsa-miR-27a-3p	21	0	0
+hsa-miR-28-5p	22	0	0
+hsa-miR-28-3p	22	0	0
+hsa-miR-29a-5p	22	0	0
+hsa-miR-29a-3p	22	0	0
+hsa-miR-30a-5p	22	0	0
+hsa-miR-30a-3p	22	0	0
+hsa-miR-31-5p	21	0	0
+hsa-miR-31-3p	22	0	0
+hsa-miR-32-5p	22	0	0
+hsa-miR-32-3p	22	0	0
+hsa-miR-33a-5p	21	0	0
+hsa-miR-33a-3p	22	0	0
+hsa-miR-92a-1-5p	23	0	0
+hsa-miR-92a-3p	22	0	0
+hsa-miR-92a-2-5p	22	0	0
+hsa-miR-93-5p	23	0	0
+hsa-miR-93-3p	22	0	0
+hsa-miR-95-5p	21	0	0
+hsa-miR-95-3p	22	0	0
+hsa-miR-96-5p	23	0	0
+hsa-miR-96-3p	22	0	0
+hsa-miR-98-5p	22	0	0
+hsa-miR-98-3p	22	0	0
+hsa-miR-99a-5p	22	0	0
+hsa-miR-99a-3p	22	0	0
+hsa-miR-100-5p	22	0	0
+hsa-miR-100-3p	22	0	0
+hsa-miR-101-5p	22	0	0
+hsa-miR-101-3p	21	0	0
+hsa-miR-29b-1-5p	24	0	0
+hsa-miR-29b-3p	23	0	0
+hsa-miR-29b-2-5p	22	0	0
+hsa-miR-103a-2-5p	23	0	0
+hsa-miR-103a-3p	23	0	0
+hsa-miR-105-5p	23	0	0
+hsa-miR-105-3p	22	0	0
+hsa-miR-106a-5p	23	0	0
+hsa-miR-106a-3p	22	0	0
+hsa-miR-107	23	0	0
+hsa-miR-16-2-3p	22	0	0
+hsa-miR-192-5p	21	0	0
+hsa-miR-192-3p	22	0	0
+hsa-miR-196a-5p	22	0	0
+hsa-miR-197-5p	23	0	0
+hsa-miR-197-3p	22	0	0
+hsa-miR-198	22	0	0
+hsa-miR-199a-5p	23	0	0
+hsa-miR-199a-3p	22	0	0
+hsa-miR-208a-5p	22	0	0
+hsa-miR-208a-3p	22	0	0
+hsa-miR-129-5p	21	0	0
+hsa-miR-129-1-3p	22	0	0
+hsa-miR-148a-5p	22	0	0
+hsa-miR-148a-3p	22	0	0
+hsa-miR-30c-5p	23	0	0
+hsa-miR-30c-2-3p	22	0	0
+hsa-miR-30d-5p	22	0	0
+hsa-miR-30d-3p	22	0	0
+hsa-miR-139-5p	23	0	0
+hsa-miR-139-3p	23	0	0
+hsa-miR-147a	20	0	0
+hsa-miR-7-5p	23	0	0
+hsa-miR-7-1-3p	22	0	0
+hsa-miR-7-2-3p	22	0	0
+hsa-miR-10a-5p	23	0	0
+hsa-miR-10a-3p	22	0	0
+hsa-miR-10b-5p	23	0	0
+hsa-miR-10b-3p	22	0	0
+hsa-miR-34a-5p	22	0	0
+hsa-miR-34a-3p	22	0	0
+hsa-miR-181a-5p	23	0	0
+hsa-miR-181a-2-3p	22	0	0
+hsa-miR-181b-5p	23	0	0
+hsa-miR-181b-3p	21	0	0
+hsa-miR-181c-5p	22	0	0
+hsa-miR-181c-3p	22	0	0
+hsa-miR-182-5p	24	0	0
+hsa-miR-182-3p	21	0	0
+hsa-miR-183-5p	22	0	0
+hsa-miR-183-3p	22	0	0
+hsa-miR-187-5p	22	0	0
+hsa-miR-187-3p	22	0	0
+hsa-miR-196a-3p	22	0	0
+hsa-miR-199b-5p	23	0	0
+hsa-miR-199b-3p	22	0	0
+hsa-miR-203a-5p	25	0	0
+hsa-miR-203a-3p	22	0	0
+hsa-miR-204-5p	22	0	0
+hsa-miR-204-3p	21	0	0
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+hsa-miR-210-5p	22	0	0
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+hsa-miR-211-3p	21	0	0
+hsa-miR-212-5p	23	0	0
+hsa-miR-212-3p	21	0	0
+hsa-miR-181a-3p	22	0	0
+hsa-miR-214-5p	22	0	0
+hsa-miR-214-3p	22	0	0
+hsa-miR-215-5p	21	0	0
+hsa-miR-215-3p	23	0	0
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+hsa-miR-218-5p	21	0	0
+hsa-miR-218-1-3p	22	0	0
+hsa-miR-218-2-3p	22	0	0
+hsa-miR-219a-5p	21	0	0
+hsa-miR-219a-1-3p	22	0	0
+hsa-miR-221-5p	22	0	0
+hsa-miR-221-3p	23	0	0
+hsa-miR-222-5p	22	0	0
+hsa-miR-222-3p	21	0	0
+hsa-miR-223-5p	22	0	0
+hsa-miR-223-3p	22	0	0
+hsa-miR-224-5p	21	0	0
+hsa-miR-224-3p	23	0	0
+hsa-miR-200b-5p	22	0	0
+hsa-miR-200b-3p	22	0	0
+hsa-let-7g-5p	22	0	0
+hsa-let-7g-3p	21	0	0
+hsa-let-7i-5p	22	0	0
+hsa-let-7i-3p	22	0	0
+hsa-miR-1-3p	22	0	0
+hsa-miR-15b-5p	22	0	0
+hsa-miR-15b-3p	22	0	0
+hsa-miR-23b-5p	22	0	0
+hsa-miR-23b-3p	21	0	0
+hsa-miR-27b-5p	22	0	0
+hsa-miR-27b-3p	21	0	0
+hsa-miR-30b-5p	22	0	0
+hsa-miR-30b-3p	22	0	0
+hsa-miR-122-5p	22	0	0
+hsa-miR-122-3p	22	0	0
+hsa-miR-124-5p	22	0	0
+hsa-miR-124-3p	20	0	0
+hsa-miR-125b-5p	22	0	0
+hsa-miR-125b-1-3p	22	0	0
+hsa-miR-128-1-5p	23	0	0
+hsa-miR-128-3p	21	0	0
+hsa-miR-130a-5p	22	0	0
+hsa-miR-130a-3p	22	0	0
+hsa-miR-132-5p	22	0	0
+hsa-miR-132-3p	22	0	0
+hsa-miR-133a-5p	22	0	0
+hsa-miR-133a-3p	22	0	0
+hsa-miR-135a-5p	23	0	0
+hsa-miR-135a-3p	22	0	0
+hsa-miR-137	23	0	0
+hsa-miR-138-5p	23	0	0
+hsa-miR-138-2-3p	22	0	0
+hsa-miR-140-5p	22	0	0
+hsa-miR-140-3p	21	0	0
+hsa-miR-141-5p	22	0	0
+hsa-miR-141-3p	22	0	0
+hsa-miR-142-5p	21	0	0
+hsa-miR-142-3p	23	0	0
+hsa-miR-143-5p	22	0	0
+hsa-miR-143-3p	21	0	0
+hsa-miR-144-5p	22	0	0
+hsa-miR-144-3p	20	0	0
+hsa-miR-145-5p	23	0	0
+hsa-miR-145-3p	22	0	0
+hsa-miR-152-5p	23	0	0
+hsa-miR-152-3p	21	0	0
+hsa-miR-153-3p	22	0	0
+hsa-miR-153-5p	22	0	0
+hsa-miR-191-5p	23	0	0
+hsa-miR-191-3p	22	0	0
+hsa-miR-9-5p	23	0	0
+hsa-miR-9-3p	22	0	0
+hsa-miR-125a-5p	24	0	0
+hsa-miR-125a-3p	22	0	0
+hsa-miR-125b-2-3p	22	0	0
+hsa-miR-126-5p	21	0	0
+hsa-miR-126-3p	22	0	0
+hsa-miR-127-5p	22	0	0
+hsa-miR-127-3p	22	0	0
+hsa-miR-129-2-3p	22	0	0
+hsa-miR-134-5p	22	0	0
+hsa-miR-134-3p	23	0	0
+hsa-miR-136-5p	23	0	0
+hsa-miR-136-3p	22	0	0
+hsa-miR-138-1-3p	22	0	0
+hsa-miR-146a-5p	22	0	0
+hsa-miR-146a-3p	22	0	0
+hsa-miR-149-5p	23	0	0
+hsa-miR-149-3p	21	0	0
+hsa-miR-150-5p	22	0	0
+hsa-miR-150-3p	22	0	0
+hsa-miR-154-5p	22	0	0
+hsa-miR-154-3p	22	0	0
+hsa-miR-184	22	0	0
+hsa-miR-185-5p	22	0	0
+hsa-miR-185-3p	22	0	0
+hsa-miR-186-5p	22	3	0
+hsa-miR-186-3p	22	0	0
+hsa-miR-188-5p	21	0	0
+hsa-miR-188-3p	21	0	0
+hsa-miR-190a-5p	22	0	0
+hsa-miR-190a-3p	21	0	0
+hsa-miR-193a-5p	22	0	0
+hsa-miR-193a-3p	22	0	0
+hsa-miR-194-5p	22	0	0
+hsa-miR-195-5p	2100	0	0
+hsa-miR-195-3p	2200	0	0
+hsa-miR-206	22	0	0
+hsa-miR-320a	22	0	0
+hsa-miR-200c-5p	22	0	0
+hsa-miR-200c-3p	23	2	0
+hsa-miR-1-5p	22	0	0
+hsa-miR-155-5p	23	0	0
+hsa-miR-155-3p	22	0	0
+hsa-miR-181b-2-3p	20	0	0
+hsa-miR-128-2-5p	23	0	0
+hsa-miR-194-3p	22	0	0
+hsa-miR-106b-5p	21	0	0
+hsa-miR-106b-3p	22	0	0
+hsa-miR-29c-5p	22	0	0
+hsa-miR-29c-3p	22	0	0
+hsa-miR-30c-1-3p	22	0	0
+hsa-miR-200a-5p	22	0	0
+hsa-miR-200a-3p	22	0	0
+hsa-miR-302a-5p	23	0	0
+hsa-miR-302a-3p	23	0	0
+hsa-miR-219a-2-3p	22	0	0
+hsa-miR-34b-5p	23	0	0
+hsa-miR-34b-3p	22	0	0
+hsa-miR-34c-5p	23	0	0
+hsa-miR-34c-3p	22	0	0
+hsa-miR-299-5p	22	0	0
+hsa-miR-299-3p	22	0	0
+hsa-miR-301a-5p	22	0	0
+hsa-miR-301a-3p	23	0	0
+hsa-miR-99b-5p	22	0	0
+hsa-miR-99b-3p	22	0	0
+hsa-miR-296-5p	21	0	0
+hsa-miR-296-3p	22	0	0
+hsa-miR-130b-5p	21	0	0
+hsa-miR-130b-3p	22	0	0
+hsa-miR-30e-5p	22	0	0
+hsa-miR-30e-3p	22	0	0
+hsa-miR-26a-2-3p	22	0	0
+hsa-miR-361-5p	22	0	0
+hsa-miR-361-3p	23	0	0
+hsa-miR-362-5p	24	0	0
+hsa-miR-362-3p	22	0	0
+hsa-miR-363-5p	22	0	0
+hsa-miR-363-3p	22	0	0
+hsa-miR-365a-5p	23	0	0
+hsa-miR-365a-3p	22	0	0
+hsa-miR-365b-5p	22	0	0
+hsa-miR-365b-3p	22	0	0
+hsa-miR-302b-5p	22	0	0
+hsa-miR-302b-3p	23	0	0
+hsa-miR-302c-5p	22	0	0
+hsa-miR-302c-3p	23	0	0
+hsa-miR-302d-5p	22	0	0
+hsa-miR-302d-3p	23	0	0
+hsa-miR-367-5p	22	0	0
+hsa-miR-367-3p	22	0	0
+hsa-miR-376c-5p	21	0	0
+hsa-miR-376c-3p	21	0	0
+hsa-miR-369-5p	22	0	0
+hsa-miR-369-3p	21	0	0
+hsa-miR-370-5p	22	0	0
+hsa-miR-370-3p	22	0	0
+hsa-miR-371a-5p	20	0	0
+hsa-miR-371a-3p	23	0	0
+hsa-miR-372-5p	23	0	0
+hsa-miR-372-3p	23	5	0
+hsa-miR-373-5p	22	0	0
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+hsa-miR-374a-3p	22	0	0
+hsa-miR-375	22	0	0
+hsa-miR-376a-5p	22	0	0
+hsa-miR-376a-3p	21	0	0
+hsa-miR-377-5p	22	0	0
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+hsa-miR-378a-3p	22	0	0
+hsa-miR-379-5p	21	0	0
+hsa-miR-379-3p	22	0	0
+hsa-miR-380-5p	22	0	0
+hsa-miR-380-3p	22	0	0
+hsa-miR-381-5p	22	0	0
+hsa-miR-381-3p	22	0	0
+hsa-miR-382-5p	22	0	0
+hsa-miR-382-3p	21	0	0
+hsa-miR-383-5p	22	0	0
+hsa-miR-383-3p	19	0	0
+hsa-miR-340-5p	22	0	0
+hsa-miR-340-3p	22	0	0
+hsa-miR-330-5p	22	0	0
+hsa-miR-330-3p	23	0	0
+hsa-miR-328-5p	23	0	0
+hsa-miR-328-3p	22	0	0
+hsa-miR-342-5p	21	0	0
+hsa-miR-342-3p	23	0	0
+hsa-miR-337-5p	21	0	0
+hsa-miR-337-3p	22	0	0
+hsa-miR-323a-5p	22	0	0
+hsa-miR-323a-3p	21	0	0
+hsa-miR-326	20	0	0
+hsa-miR-151a-5p	21	0	0
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+hsa-miR-6809-5p	22	0	0
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+hsa-miR-6815-3p	21	0	0
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+hsa-miR-6816-3p	18	0	0
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+hsa-miR-6827-3p	21	0	0
+hsa-miR-6828-5p	22	0	0
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+hsa-miR-6829-5p	20	0	0
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+hsa-miR-6832-5p	23	0	0
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+hsa-miR-6835-5p	22	0	0
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+hsa-miR-6837-5p	21	0	0
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+hsa-miR-6838-5p	22	0	0
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+hsa-miR-6842-5p	22	0	0
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+hsa-miR-6847-3p	22	0	0
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+hsa-miR-6852-5p	21	0	0
+hsa-miR-6852-3p	17	0	0
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+hsa-miR-6855-5p	25	0	0
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+hsa-miR-6856-5p	24	0	0
+hsa-miR-6856-3p	22	0	0
+hsa-miR-6857-5p	22	0	0
+hsa-miR-6857-3p	21	0	0
+hsa-miR-6858-5p	22	0	0
+hsa-miR-6858-3p	22	0	0
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+hsa-miR-6884-5p	22	0	0
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+hsa-miR-6886-5p	21	0	0
+hsa-miR-6886-3p	21	0	0
+hsa-miR-6887-5p	23	0	0
+hsa-miR-6887-3p	21	0	0
+hsa-miR-6888-5p	20	0	0
+hsa-miR-6888-3p	21	0	0
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+hsa-miR-6889-3p	20	0	0
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+hsa-miR-6890-3p	20	0	0
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+hsa-miR-7107-3p	27	0	0
+hsa-miR-7108-5p	21	2	0
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+hsa-miR-9500	19	0	0
+hsa-miR-548bb-5p	22	0	0
+hsa-miR-548bb-3p	22	0	0
+*	0	0	1713517
diff --git a/testdata/smrnaseq/counts/Control_N1_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Control_N1_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..3d601dcd
--- /dev/null
+++ b/testdata/smrnaseq/counts/Control_N1_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
+hsa-let-7a-1	80	2221	0
+hsa-let-7a-2	72	3122	0
+hsa-let-7a-3	74	59	0
+hsa-let-7b	83	1469	0
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+hsa-let-7f-2	83	465	0
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+hsa-mir-19b-2	96	31	0
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+hsa-mir-92a-1	78	416	0
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+hsa-mir-93	80	778	0
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+hsa-mir-98	119	149	0
+hsa-mir-99a	81	283	0
+hsa-mir-100	80	53	0
+hsa-mir-101-1	75	20	0
+hsa-mir-29b-1	81	1	0
+hsa-mir-29b-2	81	9	0
+hsa-mir-103a-2	78	422	0
+hsa-mir-103a-1	78	491	0
+hsa-mir-105-1	81	10	0
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diff --git a/testdata/smrnaseq/counts/Control_N2_mature.sorted.idxstats b/testdata/smrnaseq/counts/Control_N2_mature.sorted.idxstats
new file mode 100644
index 00000000..e29756fd
--- /dev/null
+++ b/testdata/smrnaseq/counts/Control_N2_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
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+hsa-miR-6876-3p	24	0	0
+hsa-miR-6877-5p	22	0	0
+hsa-miR-6877-3p	21	0	0
+hsa-miR-6878-5p	23	0	0
+hsa-miR-6878-3p	21	0	0
+hsa-miR-6879-5p	22	0	0
+hsa-miR-6879-3p	21	0	0
+hsa-miR-6880-5p	22	0	0
+hsa-miR-6880-3p	21	0	0
+hsa-miR-6881-5p	22	0	0
+hsa-miR-6881-3p	22	0	0
+hsa-miR-6882-5p	22	0	0
+hsa-miR-6882-3p	24	0	0
+hsa-miR-6883-5p	22	0	0
+hsa-miR-6883-3p	22	0	0
+hsa-miR-6884-5p	22	0	0
+hsa-miR-6884-3p	23	0	0
+hsa-miR-6885-5p	25	0	0
+hsa-miR-6885-3p	21	0	0
+hsa-miR-6886-5p	21	0	0
+hsa-miR-6886-3p	21	0	0
+hsa-miR-6887-5p	23	0	0
+hsa-miR-6887-3p	21	0	0
+hsa-miR-6888-5p	20	0	0
+hsa-miR-6888-3p	21	0	0
+hsa-miR-6889-5p	23	0	0
+hsa-miR-6889-3p	20	0	0
+hsa-miR-6890-5p	21	0	0
+hsa-miR-6890-3p	20	0	0
+hsa-miR-6891-5p	19	0	0
+hsa-miR-6891-3p	21	0	0
+hsa-miR-6892-5p	21	0	0
+hsa-miR-6892-3p	21	0	0
+hsa-miR-6893-5p	21	0	0
+hsa-miR-6893-3p	22	0	0
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+hsa-miR-7106-5p	20	0	0
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+hsa-miR-7107-5p	22	0	0
+hsa-miR-7107-3p	27	0	0
+hsa-miR-7108-5p	21	0	0
+hsa-miR-7108-3p	20	0	0
+hsa-miR-7109-5p	21	0	0
+hsa-miR-7109-3p	22	0	0
+hsa-miR-7110-5p	21	0	0
+hsa-miR-7110-3p	22	0	0
+hsa-miR-7111-5p	22	0	0
+hsa-miR-7111-3p	22	0	0
+hsa-miR-7112-5p	22	0	0
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+hsa-miR-7113-5p	21	0	0
+hsa-miR-7113-3p	23	0	0
+hsa-miR-7114-5p	21	0	0
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+hsa-miR-7152-3p	20	0	0
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+hsa-miR-7153-3p	18	0	0
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+hsa-miR-7162-5p	18	0	0
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+hsa-miR-7853-5p	21	0	0
+hsa-miR-7854-3p	21	0	0
+hsa-miR-7855-5p	22	0	0
+hsa-miR-7856-5p	21	0	0
+hsa-miR-548ba	22	0	0
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+hsa-miR-8057	21	0	0
+hsa-miR-8058	22	0	0
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+hsa-miR-8063	22	0	0
+hsa-miR-8064	20	0	0
+hsa-miR-8065	24	0	0
+hsa-miR-8066	21	0	0
+hsa-miR-8067	22	0	0
+hsa-miR-8068	22	0	0
+hsa-miR-8069	23	0	0
+hsa-miR-8070	22	0	0
+hsa-miR-8071	20	0	0
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+hsa-miR-8074	24	0	0
+hsa-miR-8075	24	0	0
+hsa-miR-8076	24	0	0
+hsa-miR-8077	22	0	0
+hsa-miR-8078	23	0	0
+hsa-miR-8079	20	0	0
+hsa-miR-8080	23	0	0
+hsa-miR-8081	23	0	0
+hsa-miR-8082	22	0	0
+hsa-miR-8083	21	0	0
+hsa-miR-8084	23	0	0
+hsa-miR-8085	21	0	0
+hsa-miR-8086	22	0	0
+hsa-miR-8087	23	0	0
+hsa-miR-8088	21	0	0
+hsa-miR-8089	24	0	0
+hsa-miR-8485	21	0	0
+hsa-miR-9500	19	0	0
+hsa-miR-548bb-5p	22	0	0
+hsa-miR-548bb-3p	22	0	0
+*	0	0	670172
diff --git a/testdata/smrnaseq/counts/Control_N2_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Control_N2_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..89bd5773
--- /dev/null
+++ b/testdata/smrnaseq/counts/Control_N2_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
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+hsa-mir-8062	85	0	0
+hsa-mir-8063	81	0	0
+hsa-mir-8064	90	0	0
+hsa-mir-8065	100	0	0
+hsa-mir-8066	78	0	0
+hsa-mir-8067	77	0	0
+hsa-mir-8068	68	0	0
+hsa-mir-8069-1	86	0	0
+hsa-mir-8070	88	0	0
+hsa-mir-8071-1	65	0	0
+hsa-mir-8072	80	0	0
+hsa-mir-8073	72	0	0
+hsa-mir-8074	81	0	0
+hsa-mir-8075	80	0	0
+hsa-mir-8076	83	0	0
+hsa-mir-8077	75	0	0
+hsa-mir-8078	84	0	0
+hsa-mir-8079	72	0	0
+hsa-mir-8080	89	0	0
+hsa-mir-8081	95	0	0
+hsa-mir-8082	81	0	0
+hsa-mir-8083	89	0	0
+hsa-mir-8084	89	0	0
+hsa-mir-8085	65	0	0
+hsa-mir-8086	93	1	0
+hsa-mir-8087	78	0	0
+hsa-mir-8088	86	0	0
+hsa-mir-8089	82	0	0
+hsa-mir-6862-2	70	0	0
+hsa-mir-8071-2	65	0	0
+hsa-mir-6770-2	60	0	0
+hsa-mir-6770-3	60	0	0
+hsa-mir-6859-2	68	0	0
+hsa-mir-6859-3	68	0	0
+hsa-mir-8485	91	0	0
+hsa-mir-9500	65	0	0
+hsa-mir-548bb	66	0	0
+hsa-mir-3179-4	84	0	0
+hsa-mir-1244-4	85	0	0
+hsa-mir-3648-2	180	0	0
+hsa-mir-3670-3	65	0	0
+hsa-mir-3670-4	65	0	0
+hsa-mir-3687-2	61	0	0
+hsa-mir-6724-2	92	0	0
+hsa-mir-6724-3	92	0	0
+hsa-mir-6724-4	92	0	0
+hsa-mir-8069-2	86	0	0
+hsa-mir-941-5	72	0	0
+hsa-mir-6859-4	68	0	0
+hsa-mir-5701-3	82	0	0
+*	0	0	667657
diff --git a/testdata/smrnaseq/counts/Control_N3_mature.sorted.idxstats b/testdata/smrnaseq/counts/Control_N3_mature.sorted.idxstats
new file mode 100644
index 00000000..ab72cc01
--- /dev/null
+++ b/testdata/smrnaseq/counts/Control_N3_mature.sorted.idxstats
@@ -0,0 +1,2589 @@
+hsa-let-7a-5p	22	0	0
+hsa-let-7a-3p	21	0	0
+hsa-let-7a-2-3p	22	0	0
+hsa-let-7b-5p	22	0	0
+hsa-let-7b-3p	22	0	0
+hsa-let-7c-5p	22	0	0
+hsa-let-7c-3p	22	0	0
+hsa-let-7d-5p	22	0	0
+hsa-let-7d-3p	22	0	0
+hsa-let-7e-5p	22	0	0
+hsa-let-7e-3p	22	0	0
+hsa-let-7f-5p	22	0	0
+hsa-let-7f-1-3p	22	0	0
+hsa-let-7f-2-3p	22	0	0
+hsa-miR-15a-5p	22	0	0
+hsa-miR-15a-3p	22	0	0
+hsa-miR-16-5p	22	0	0
+hsa-miR-16-1-3p	22	0	0
+hsa-miR-17-5p	23	0	0
+hsa-miR-17-3p	22	0	0
+hsa-miR-18a-5p	23	0	0
+hsa-miR-18a-3p	23	0	0
+hsa-miR-19a-5p	22	0	0
+hsa-miR-19a-3p	23	0	0
+hsa-miR-19b-1-5p	23	0	0
+hsa-miR-19b-3p	23	0	0
+hsa-miR-19b-2-5p	22	0	0
+hsa-miR-20a-5p	23	0	0
+hsa-miR-20a-3p	22	0	0
+hsa-miR-21-5p	22	0	0
+hsa-miR-21-3p	21	0	0
+hsa-miR-22-5p	22	0	0
+hsa-miR-22-3p	22	0	0
+hsa-miR-23a-5p	22	0	0
+hsa-miR-23a-3p	21	0	0
+hsa-miR-24-1-5p	22	0	0
+hsa-miR-24-3p	22	0	0
+hsa-miR-24-2-5p	22	0	0
+hsa-miR-25-5p	21	0	0
+hsa-miR-25-3p	22	0	0
+hsa-miR-26a-5p	22	0	0
+hsa-miR-26a-1-3p	22	0	0
+hsa-miR-26b-5p	21	0	0
+hsa-miR-26b-3p	22	0	0
+hsa-miR-27a-5p	22	0	0
+hsa-miR-27a-3p	21	0	0
+hsa-miR-28-5p	22	0	0
+hsa-miR-28-3p	22	0	0
+hsa-miR-29a-5p	22	0	0
+hsa-miR-29a-3p	22	0	0
+hsa-miR-30a-5p	22	0	0
+hsa-miR-30a-3p	22	0	0
+hsa-miR-31-5p	21	0	0
+hsa-miR-31-3p	22	0	0
+hsa-miR-32-5p	22	0	0
+hsa-miR-32-3p	22	0	0
+hsa-miR-33a-5p	21	0	0
+hsa-miR-33a-3p	22	0	0
+hsa-miR-92a-1-5p	23	0	0
+hsa-miR-92a-3p	22	0	0
+hsa-miR-92a-2-5p	22	0	0
+hsa-miR-93-5p	23	0	0
+hsa-miR-93-3p	22	0	0
+hsa-miR-95-5p	21	0	0
+hsa-miR-95-3p	22	0	0
+hsa-miR-96-5p	23	0	0
+hsa-miR-96-3p	22	0	0
+hsa-miR-98-5p	22	0	0
+hsa-miR-98-3p	22	0	0
+hsa-miR-99a-5p	22	0	0
+hsa-miR-99a-3p	22	0	0
+hsa-miR-100-5p	22	0	0
+hsa-miR-100-3p	22	0	0
+hsa-miR-101-5p	22	0	0
+hsa-miR-101-3p	21	0	0
+hsa-miR-29b-1-5p	24	0	0
+hsa-miR-29b-3p	23	0	0
+hsa-miR-29b-2-5p	22	0	0
+hsa-miR-103a-2-5p	23	0	0
+hsa-miR-103a-3p	23	0	0
+hsa-miR-105-5p	23	0	0
+hsa-miR-105-3p	22	0	0
+hsa-miR-106a-5p	23	0	0
+hsa-miR-106a-3p	22	0	0
+hsa-miR-107	23	0	0
+hsa-miR-16-2-3p	22	0	0
+hsa-miR-192-5p	21	0	0
+hsa-miR-192-3p	22	0	0
+hsa-miR-196a-5p	22	0	0
+hsa-miR-197-5p	23	0	0
+hsa-miR-197-3p	22	0	0
+hsa-miR-198	22	0	0
+hsa-miR-199a-5p	23	0	0
+hsa-miR-199a-3p	22	0	0
+hsa-miR-208a-5p	22	0	0
+hsa-miR-208a-3p	22	0	0
+hsa-miR-129-5p	21	0	0
+hsa-miR-129-1-3p	22	0	0
+hsa-miR-148a-5p	22	0	0
+hsa-miR-148a-3p	22	0	0
+hsa-miR-30c-5p	23	0	0
+hsa-miR-30c-2-3p	22	0	0
+hsa-miR-30d-5p	22	0	0
+hsa-miR-30d-3p	22	0	0
+hsa-miR-139-5p	23	0	0
+hsa-miR-139-3p	23	0	0
+hsa-miR-147a	20	0	0
+hsa-miR-7-5p	23	0	0
+hsa-miR-7-1-3p	22	0	0
+hsa-miR-7-2-3p	22	0	0
+hsa-miR-10a-5p	23	0	0
+hsa-miR-10a-3p	22	0	0
+hsa-miR-10b-5p	23	0	0
+hsa-miR-10b-3p	22	0	0
+hsa-miR-34a-5p	22	0	0
+hsa-miR-34a-3p	22	0	0
+hsa-miR-181a-5p	23	0	0
+hsa-miR-181a-2-3p	22	0	0
+hsa-miR-181b-5p	23	0	0
+hsa-miR-181b-3p	21	0	0
+hsa-miR-181c-5p	22	0	0
+hsa-miR-181c-3p	22	0	0
+hsa-miR-182-5p	24	0	0
+hsa-miR-182-3p	21	0	0
+hsa-miR-183-5p	22	0	0
+hsa-miR-183-3p	22	0	0
+hsa-miR-187-5p	22	0	0
+hsa-miR-187-3p	22	0	0
+hsa-miR-196a-3p	22	0	0
+hsa-miR-199b-5p	23	0	0
+hsa-miR-199b-3p	22	0	0
+hsa-miR-203a-5p	25	0	0
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+hsa-miR-204-5p	22	0	0
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+hsa-miR-219a-5p	21	0	0
+hsa-miR-219a-1-3p	22	0	0
+hsa-miR-221-5p	22	0	0
+hsa-miR-221-3p	23	0	0
+hsa-miR-222-5p	22	0	0
+hsa-miR-222-3p	21	0	0
+hsa-miR-223-5p	22	0	0
+hsa-miR-223-3p	22	0	0
+hsa-miR-224-5p	21	0	0
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+hsa-miR-200b-5p	22	0	0
+hsa-miR-200b-3p	22	0	0
+hsa-let-7g-5p	22	0	0
+hsa-let-7g-3p	21	0	0
+hsa-let-7i-5p	22	0	0
+hsa-let-7i-3p	22	0	0
+hsa-miR-1-3p	22	0	0
+hsa-miR-15b-5p	22	0	0
+hsa-miR-15b-3p	22	0	0
+hsa-miR-23b-5p	22	0	0
+hsa-miR-23b-3p	21	0	0
+hsa-miR-27b-5p	22	0	0
+hsa-miR-27b-3p	21	0	0
+hsa-miR-30b-5p	22	0	0
+hsa-miR-30b-3p	22	0	0
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+hsa-miR-122-3p	22	0	0
+hsa-miR-124-5p	22	0	0
+hsa-miR-124-3p	20	0	0
+hsa-miR-125b-5p	22	0	0
+hsa-miR-125b-1-3p	22	0	0
+hsa-miR-128-1-5p	23	0	0
+hsa-miR-128-3p	21	0	0
+hsa-miR-130a-5p	22	0	0
+hsa-miR-130a-3p	22	0	0
+hsa-miR-132-5p	22	0	0
+hsa-miR-132-3p	22	0	0
+hsa-miR-133a-5p	22	0	0
+hsa-miR-133a-3p	22	0	0
+hsa-miR-135a-5p	23	0	0
+hsa-miR-135a-3p	22	0	0
+hsa-miR-137	23	0	0
+hsa-miR-138-5p	23	0	0
+hsa-miR-138-2-3p	22	0	0
+hsa-miR-140-5p	22	0	0
+hsa-miR-140-3p	21	0	0
+hsa-miR-141-5p	22	0	0
+hsa-miR-141-3p	22	0	0
+hsa-miR-142-5p	21	0	0
+hsa-miR-142-3p	23	0	0
+hsa-miR-143-5p	22	0	0
+hsa-miR-143-3p	21	0	0
+hsa-miR-144-5p	22	0	0
+hsa-miR-144-3p	20	0	0
+hsa-miR-145-5p	23	0	0
+hsa-miR-145-3p	22	0	0
+hsa-miR-152-5p	23	0	0
+hsa-miR-152-3p	21	0	0
+hsa-miR-153-3p	22	0	0
+hsa-miR-153-5p	22	0	0
+hsa-miR-191-5p	23	2	0
+hsa-miR-191-3p	22	0	0
+hsa-miR-9-5p	23	0	0
+hsa-miR-9-3p	22	0	0
+hsa-miR-125a-5p	24	0	0
+hsa-miR-125a-3p	22	0	0
+hsa-miR-125b-2-3p	22	0	0
+hsa-miR-126-5p	21	0	0
+hsa-miR-126-3p	22	0	0
+hsa-miR-127-5p	22	0	0
+hsa-miR-127-3p	22	0	0
+hsa-miR-129-2-3p	22	0	0
+hsa-miR-134-5p	22	0	0
+hsa-miR-134-3p	23	0	0
+hsa-miR-136-5p	23	0	0
+hsa-miR-136-3p	22	0	0
+hsa-miR-138-1-3p	22	0	0
+hsa-miR-146a-5p	22	0	0
+hsa-miR-146a-3p	22	0	0
+hsa-miR-149-5p	23	0	0
+hsa-miR-149-3p	21	0	0
+hsa-miR-150-5p	22	0	0
+hsa-miR-150-3p	22	0	0
+hsa-miR-154-5p	22	0	0
+hsa-miR-154-3p	22	0	0
+hsa-miR-184	22	0	0
+hsa-miR-185-5p	22	0	0
+hsa-miR-185-3p	22	0	0
+hsa-miR-186-5p	22	0	0
+hsa-miR-186-3p	22	0	0
+hsa-miR-188-5p	21	0	0
+hsa-miR-188-3p	21	0	0
+hsa-miR-190a-5p	22	0	0
+hsa-miR-190a-3p	21	0	0
+hsa-miR-193a-5p	22	0	0
+hsa-miR-193a-3p	22	0	0
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+hsa-miR-195-5p	21	0	0
+hsa-miR-195-3p	22	0	0
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+hsa-miR-320a	22	0	0
+hsa-miR-200c-5p	22	0	0
+hsa-miR-200c-3p	23	0	0
+hsa-miR-1-5p	22	0	0
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+hsa-miR-181b-2-3p	20	0	0
+hsa-miR-128-2-5p	23	0	0
+hsa-miR-194-3p	22	0	0
+hsa-miR-106b-5p	21	0	0
+hsa-miR-106b-3p	22	0	0
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+hsa-miR-29c-3p	22	0	0
+hsa-miR-30c-1-3p	22	0	0
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+hsa-miR-200a-3p	22	0	0
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+hsa-miR-302a-3p	23	0	0
+hsa-miR-219a-2-3p	22	0	0
+hsa-miR-34b-5p	23	0	0
+hsa-miR-34b-3p	22	0	0
+hsa-miR-34c-5p	23	0	0
+hsa-miR-34c-3p	22	0	0
+hsa-miR-299-5p	22	0	0
+hsa-miR-299-3p	22	0	0
+hsa-miR-301a-5p	22	0	0
+hsa-miR-301a-3p	23	0	0
+hsa-miR-99b-5p	22	0	0
+hsa-miR-99b-3p	22	0	0
+hsa-miR-296-5p	21	0	0
+hsa-miR-296-3p	22	0	0
+hsa-miR-130b-5p	21	0	0
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+hsa-miR-30e-3p	22	0	0
+hsa-miR-26a-2-3p	22	0	0
+hsa-miR-361-5p	22	0	0
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+hsa-miR-362-5p	24	0	0
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+hsa-miR-363-3p	22	0	0
+hsa-miR-365a-5p	23	0	0
+hsa-miR-365a-3p	22	0	0
+hsa-miR-365b-5p	22	0	0
+hsa-miR-365b-3p	22	0	0
+hsa-miR-302b-5p	22	0	0
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+hsa-miR-302c-5p	22	0	0
+hsa-miR-302c-3p	23	0	0
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+hsa-miR-376c-3p	21	0	0
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+hsa-miR-342-5p	21	0	0
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+hsa-miR-151a-5p	21	0	0
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+hsa-miR-135b-3p	22	0	0
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+hsa-miR-384	20	0	0
+hsa-miR-196b-5p	22	0	0
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+hsa-miR-423-5p	23	0	0
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+hsa-miR-424-5p	22	0	0
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+hsa-miR-18b-5p	23	0	0
+hsa-miR-18b-3p	22	0	0
+hsa-miR-20b-5p	23	0	0
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+hsa-miR-6857-5p	22	0	0
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+hsa-miR-548bb-5p	22	0	0
+hsa-miR-548bb-3p	22	0	0
+*	0	0	2690903
diff --git a/testdata/smrnaseq/counts/Control_N3_mature_hairpin.sorted.idxstats b/testdata/smrnaseq/counts/Control_N3_mature_hairpin.sorted.idxstats
new file mode 100644
index 00000000..9e2fa443
--- /dev/null
+++ b/testdata/smrnaseq/counts/Control_N3_mature_hairpin.sorted.idxstats
@@ -0,0 +1,1882 @@
+hsa-let-7a-1	80	2625	0
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diff --git a/testdata/smrnaseq/design.txt b/testdata/smrnaseq/design.txt
new file mode 100644
index 00000000..4983798f
--- /dev/null
+++ b/testdata/smrnaseq/design.txt
@@ -0,0 +1 @@
+~ batch + condition_treatment
diff --git a/testdata/smrnaseq/requested_genes.txt b/testdata/smrnaseq/requested_genes.txt
new file mode 100644
index 00000000..22e59997
--- /dev/null
+++ b/testdata/smrnaseq/requested_genes.txt
@@ -0,0 +1,5 @@
+hsa-mir-100
+hsa-mir-125b-1
+hsa-mir-200a
+hsa-mir-505
+hsa-let-7c
diff --git a/testdata/smrnaseq/samplesheet.tsv b/testdata/smrnaseq/samplesheet.tsv
new file mode 100644
index 00000000..ddd07d13
--- /dev/null
+++ b/testdata/smrnaseq/samplesheet.tsv
@@ -0,0 +1,9 @@
+QBiC Code	Condition: treatment	batch	Secondary Name
+Clone1_NN1	clone1	1	1
+Clone1_NN3	clone1	3	2
+Clone9_NN1	clone9	1	3
+Clone9_NN2	clone9	2	4
+Clone9_NN3	clone9	3	5
+Control_N1	control	1	6
+Control_N2	control	2	7
+Control_N3	control	3	8
diff --git a/testdata/software_versions_smrnaseq.yml b/testdata/software_versions_smrnaseq.yml
new file mode 100644
index 00000000..2c314188
--- /dev/null
+++ b/testdata/software_versions_smrnaseq.yml
@@ -0,0 +1,64 @@
+BOWTIE_MAP_GENOME:
+  bowtie: 1.3.1
+  samtools: '1.14'
+BOWTIE_MAP_HAIRPIN:
+  bowtie: 1.3.1
+  samtools: '1.14'
+BOWTIE_MAP_MATURE:
+  bowtie: 1.3.1
+  samtools: '1.14'
+BOWTIE_MAP_SEQCLUSTER:
+  bowtie: 1.3.1
+  samtools: '1.14'
+CUSTOM_DUMPSOFTWAREVERSIONS:
+  python: 3.11.0
+  yaml: '6.0'
+FASTP:
+  fastp: 0.23.2
+FASTQC_RAW:
+  fastqc: 0.11.9
+FASTQC_TRIM:
+  fastqc: 0.11.9
+FORMAT_HAIRPIN:
+  fastx_toolkit: 0.0.14
+FORMAT_MATURE:
+  fastx_toolkit: 0.0.14
+INDEX_GENOME:
+  bowtie: 1.3.1
+INDEX_HAIRPIN:
+  bowtie: 1.3.1
+INDEX_MATURE:
+  bowtie: 1.3.1
+MIRDEEP2_MAPPER:
+  mapper: 2.0.1
+MIRDEEP2_PIGZ":
+  pigz: 2.3.4
+MIRDEEP2_RUN":
+  mirdeep2: 2.0.1
+MIRTOP_QUANT":
+  mirtop: 0.4.25
+MIRTRACE_RUN":
+  mirtrace: 1.0.1
+PARSE_HAIRPIN":
+  seqkit: 2.3.0
+PARSE_MATURE":
+  seqkit: 2.3.0
+SAMPLESHEET_CHECK:
+  python: 3.8.3
+SAMTOOLS_FLAGSTAT:
+  samtools: '1.17'
+SAMTOOLS_IDXSTATS:
+  samtools: '1.17'
+SAMTOOLS_INDEX:
+  samtools: '1.17'
+SAMTOOLS_SORT:
+  samtools: '1.17'
+SAMTOOLS_STATS:
+  samtools: '1.17'
+SEQCLUSTER_SEQUENCES":
+  seqcluster: 1.2.9
+TABLE_MERGE:
+  r-base: 3.6.2
+Workflow:
+  Nextflow: 22.10.2
+  nf-core/smrnaseq: 2.2.1
diff --git a/tests/test_smrnaseq.yml b/tests/test_smrnaseq.yml
new file mode 100644
index 00000000..31beedd6
--- /dev/null
+++ b/tests/test_smrnaseq.yml
@@ -0,0 +1,89 @@
+- name: Run test profile with smrnaseq
+  command: nextflow run main.nf -profile test_smrnaseq,docker --citest true --round_DE 3
+  tags:
+    - test_smrnaseq
+  files:
+    - path: results_test/differential_gene_expression/metadata/smrnaseq_files.txt
+      md5sum: ce3cc117fc953a8ff4d17d0118123faf
+    - path: results_test/differential_gene_expression/DE_genes_tables/DE_contrast_condition_treatment_clone9_vs_clone1.tsv
+      md5sum: 46ca6c2ec1046e088853c96b28cd30e3
+    - path: results_test/differential_gene_expression/DE_genes_tables/DE_contrast_condition_treatment_control_vs_clone1.tsv
+      md5sum: 74214d33037aeded1bd0c839973a9e4c
+    - path: results_test/differential_gene_expression/final_gene_table/final_DE_gene_list.tsv
+      md5sum: 9f4950203e56a94235b00a1d554fa78c
+    - path: results_test/differential_gene_expression/gene_counts_tables/deseq2_library_scaled_gene_counts.tsv
+    - path: results_test/differential_gene_expression/gene_counts_tables/raw_gene_counts.tsv
+    - path: results_test/differential_gene_expression/gene_counts_tables/rlog_transformed_gene_counts.tsv
+    - path: results_test/differential_gene_expression/gene_counts_tables/sizeFactor_libraries.tsv
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-LET-7C_hsa-let-7c.pdf
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-LET-7C_hsa-let-7c.png
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-LET-7C_hsa-let-7c.svg
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-100_hsa-mir-100.pdf
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-100_hsa-mir-100.png
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-100_hsa-mir-100.svg
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-125B-1_hsa-mir-125b-1.pdf
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-125B-1_hsa-mir-125b-1.png
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-125B-1_hsa-mir-125b-1.svg
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-200A_hsa-mir-200a.pdf
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-200A_hsa-mir-200a.png
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-200A_hsa-mir-200a.svg
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-505_hsa-mir-505.pdf
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-505_hsa-mir-505.png
+    - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/HSA-MIR-505_hsa-mir-505.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_treatment_clone9_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_treatment_clone9_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_treatment_clone9_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_treatment_control_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_treatment_control_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_treatment_control_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_treatment_clone9_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_treatment_clone9_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_treatment_clone9_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_treatment_control_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_treatment_control_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_treatment_control_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/number.of.rejections_condition_treatment_clone9_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/number.of.rejections_condition_treatment_clone9_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/number.of.rejections_condition_treatment_clone9_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/number.of.rejections_condition_treatment_control_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/number.of.rejections_condition_treatment_control_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/number.of.rejections_condition_treatment_control_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Cooks-distances.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Cooks-distances.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Cooks-distances.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/dependency_small.pval_mean_normal.counts_condition_treatment_clone9_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/dependency_small.pval_mean_normal.counts_condition_treatment_clone9_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/dependency_small.pval_mean_normal.counts_condition_treatment_clone9_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/dependency_small.pval_mean_normal.counts_condition_treatment_control_vs_clone1.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/dependency_small.pval_mean_normal.counts_condition_treatment_control_vs_clone1.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/dependency_small.pval_mean_normal.counts_condition_treatment_control_vs_clone1.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Dispersion_plot.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Dispersion_plot.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Dispersion_plot.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Effects_of_transformations_on_the_variance.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Effects_of_transformations_on_the_variance.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/Effects_of_transformations_on_the_variance.svg
+    - path: results_test/differential_gene_expression/plots/Heatmaps_of_distances.pdf
+    - path: results_test/differential_gene_expression/plots/Heatmaps_of_distances.png
+    - path: results_test/differential_gene_expression/plots/Heatmaps_of_distances.svg
+    - path: results_test/differential_gene_expression/plots/PCA_plot.pdf
+    - path: results_test/differential_gene_expression/plots/PCA_plot.png
+    - path: results_test/differential_gene_expression/plots/PCA_plot.svg
+    - path: results_test/differential_gene_expression/plots/PCA_plot_with_labels.pdf
+    - path: results_test/differential_gene_expression/plots/PCA_plot_with_labels.png
+    - path: results_test/differential_gene_expression/plots/PCA_plot_with_labels.svg
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_plot.pdf
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_plot.png
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_plot.svg
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_KEGG_pathway_enrichment_results.tsv
+      md5sum: b5c4c68a304f08a54b2b9d8969334e8c
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_clone9_vs_clone1/DE_contrast_condition_treatment_clone9_vs_clone1_pathway_enrichment_results.tsv
+      md5sum: ab088ff01a4e3991be8a424e676afcdf
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_control_vs_clone1/DE_contrast_condition_treatment_control_vs_clone1_KEGG_pathway_enrichment_plot.pdf
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_control_vs_clone1/DE_contrast_condition_treatment_control_vs_clone1_KEGG_pathway_enrichment_plot.png
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_control_vs_clone1/DE_contrast_condition_treatment_control_vs_clone1_KEGG_pathway_enrichment_plot.svg
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_control_vs_clone1/DE_contrast_condition_treatment_control_vs_clone1_KEGG_pathway_enrichment_results.tsv
+      md5sum: 4a2ed390ae3e9fea628bd9c014e88cc6
+    - path: results_test/pathway_analysis/DE_contrast_condition_treatment_control_vs_clone1/DE_contrast_condition_treatment_control_vs_clone1_pathway_enrichment_results.tsv
+      md5sum: db2149ba5f2dbb6d4aed3f6284072f39
+    - path: results_test/RNAseq_report.html
diff --git a/tests/test_star_salmon.yml b/tests/test_star_salmon.yml
index 20b498cc..dbe49c9a 100644
--- a/tests/test_star_salmon.yml
+++ b/tests/test_star_salmon.yml
@@ -19,15 +19,15 @@
     - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/IL10_ENSG00000136634.pdf
     - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/IL10_ENSG00000136634.png
     - path: results_test/differential_gene_expression/plots/boxplots_requested_genes/IL10_ENSG00000136634.svg
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_H1_vs_GM12878.pdf
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_H1_vs_GM12878.png
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_H1_vs_GM12878.svg
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_K562_vs_GM12878.pdf
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_K562_vs_GM12878.png
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_K562_vs_GM12878.svg
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_MCF7_vs_GM12878.pdf
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_MCF7_vs_GM12878.png
-    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots//all_results_MA_plot_condition_cellline_MCF7_vs_GM12878.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_H1_vs_GM12878.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_H1_vs_GM12878.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_H1_vs_GM12878.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_K562_vs_GM12878.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_K562_vs_GM12878.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_K562_vs_GM12878.svg
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_MCF7_vs_GM12878.pdf
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_MCF7_vs_GM12878.png
+    - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/all_results_MA_plot_condition_cellline_MCF7_vs_GM12878.svg
     - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_cellline_H1_vs_GM12878.pdf
     - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_cellline_H1_vs_GM12878.png
     - path: results_test/differential_gene_expression/plots/further_diagnostics_plots/histogram_of_p.values_condition_cellline_H1_vs_GM12878.svg
diff --git a/workflows/rnadeseq.nf b/workflows/rnadeseq.nf
index f9b73a9c..ffbbde2c 100644
--- a/workflows/rnadeseq.nf
+++ b/workflows/rnadeseq.nf
@@ -15,7 +15,7 @@ def checkPathParamList = [
 for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } }
 
 // Check mandatory parameters
-if (!(params.input_type in ["featurecounts", "salmon", "rsem"])) { exit 1, 'Wrong input type ' + params.input_type + ', must be one of "featurecounts", "salmon", "rsem"!' }
+if (!(params.input_type in ["featurecounts", "salmon", "rsem", "smrnaseq"])) { exit 1, 'Wrong input type ' + params.input_type + ', must be one of "featurecounts", "salmon", "rsem", "smrnaseq"!' }
 
 ch_counts_path = Channel.fromPath(params.gene_counts)
 ch_metadata_file = Channel.fromPath(params.input)