add Dragmap

.github/workflows/main.yml

@@ -60,7 +60,7 @@ jobs:
       - name: test short single
         run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf
       - name: test short single cram
-        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --cram
+        run: nextflow run -ansi-log -profile docker,test_illumina_single aline.nf --cram --filter_unmapped
       - name: test short paired
         run: nextflow run -ansi-log -profile docker,test_illumina_paired aline.nf
       - name: test ont

README.md

@@ -91,6 +91,7 @@ It is then translated to the correct option in the following aligners:
 | bwamem | 🚫 | 🚫 | 🚫 |
 | bwamem2 | 🚫 | 🚫 | 🚫 |
 | bwasw | 🚫 | 🚫 | 🚫 |
+| dragmap | 🚫 | 🚫 | 🚫 |
 | graphmap2 | 🚫 | 🚫 | 🚫 |
 | hisat2 | --rna-strandness [ F / R / FR / RF ] | SF / SR / ISF OSF MSF / ISR OSR MSR | strand information |
 | hisat2 | --fr / --rf / --ff | I / O / M | read orientation |
@@ -128,6 +129,7 @@ If you provide an annotation file the pipeline will pass automatically the file
 | bwamem | 🚫 |
 | bwamem2 | 🚫 |
 | bwasw | 🚫 |
+| dragmap | 🚫 |
 | graphmap2 | GTF (--gtf)  |
 | hisat2 | 🚫 |
 | kallisto | 🚫 |
@@ -335,9 +337,8 @@ On success you should get a message looking like this:
                                         control1,path/to/data1.fastq.gz,,auto,short_single,rna
                                         control2,path/to/data2_R1.fastq.gz,path/to/data2_R2.fastq.gz,auto,short_paired,rna
         --reference                 path to the reference file (fa, fa.gz, fasta or fasta.gz)
-        --aligner                   aligner(s) to use among this list (comma or space separated) [bbmap, bowtie, bowtie2, bwaaln, bwamem, bwamem2, bwasw, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, star, subread, sublong]
+        --aligner                   aligner(s) to use among this list (comma or space separated) [bbmap, bowtie, bowtie2, bwaaln, bwamem, bwamem2, bwasw, dragmap, graphmap2, hisat2, kallisto, minimap2, novoalign, nucmer, ngmlr, salmon, star, subread, sublong]
         --outdir                    path to the output directory (default: alignment_results)
-        --cram                      output alignment files in sorted CRAM format instead of sorted BAM (default: false). This saves disk space but disables FastQC on alignment files.
         --annotation                [Optional][used by graphmap2, STAR, subread] Absolute path to the annotation file (gtf or gff3)
 
     Type of input reads
@@ -354,6 +355,8 @@ On success you should get a message looking like this:
         --trimming_fastp            run fastp for trimming (default: false)
         --fastqc                    run fastqc on raw and aligned reads (default: false). Note: FastQC will be automatically disabled for alignment files when --cram is enabled.
         --samtools_stats            run samtools stats on aligned reads (default: false)
+        --filter_unmapped           filter out unmapped reads from final alignment files (default: false). Filtering is performed during sorting when possible for optimal performance.
+        --cram                      output alignment files in sorted CRAM format instead of sorted BAM (default: false). This saves disk space but disables FastQC on alignment files. Conversion is performed during sorting when possible for optimal performance.
         --multiqc_config            path to the multiqc config file (default: config/multiqc_conf.yml)
 
     Aligner specific options
@@ -364,6 +367,7 @@ On success you should get a message looking like this:
         --bwamem_options            additional options for bwamem
         --bwamem2_options           additional options for bwamem2
         --bwasw_options             additional options for bwasw
+        --dragmap_options           additional options for dragmap
         --graphmap2_options         additional options for graphmap2
         --hisat2_options            additional options for hisat2
         --kallisto_options          additional options for kallisto
@@ -452,7 +456,8 @@ Here the description of typical ouput you will get from AliNe:
     │
     └── MultiQC                                               # MultiQC folder that aggregate results across many samples into a single report
         ├── multiqc_report.html                               # Report with interactive plots for statistics across many samples.
-        └── multiqc_report_data                               # Plot and data used by the multiqc_report.html
+        ├── multiqc_report_data                               # Plot and data used by the multiqc_report.html
+        └── alignment_comparison.tsv                          # A tsv table summerizing the statistics of the different aligners across all samples.
 ```
 
 ### Statistics
@@ -497,52 +502,7 @@ Some information produced via FastQC or Samtools stats are reported at the top o
 
 <img src="img/multiqc.png" />
 
-In order to facilitate the reading of this `General Statistics` you can export the table in tsv using the `Export as CSV...` button and execute the following piece of R code on the downloaded `general_stats_table.tsv` file :
-
-```R
-# install packages
-install.packages("dplyr")
-install.packages("stringr")
-install.packages("tidyr")
-install.packages("knitr")
-
-# Load necessary libraries
-library(dplyr)
-library(stringr)
-library(tidyr)
-library(knitr)
-
-# Read the TSV file
-file_path <- "general_stats_table.tsv"
-df <- read.delim(file_path, check.names = FALSE)
-
-# clean sample name to remove suffix _*_samtoolsstats
-df$Sample <- df$Sample |> stringr::str_remove_all("_\\d+_samtoolsstats")
-
-# sample name as row name
-rownames(df) <- df$Sample
-
-# remove Sample column and clean up the column names
-tableout <- cbind(ID = rownames(df), stack(df[-1])) |> 
-  transform(ind = as.character(ind) |> stringr::str_remove_all("\\.\\d+"))
-
-# remove na values
-tableout <- tableout[!is.na(tableout$values),]
-# remove . values
-tableout$values <- tableout$values |> stringr::str_remove_all("^\\.$")
-
-# pivot data
-tableout <- tableout |> pivot_wider(id_cols = ID , names_from = ind, values_from = values, 
-              values_fn = \(x) paste(unique(x), collapse = ""))
-
-# round each value to 4 decimals
-tableout <- tableout |> mutate(across(-ID, ~round(as.numeric(.), 4)))
-
-# print with nice output
-knitr::kable(tableout)
-```
-
-You will get a table similar to this one:  
+To make the General Statistics easier to read and compare, AliNe also generates a TSV file named `alignment_comparison.tsv`, located in the `<output_directory>/MultiQC` directory. This file contains the same information as the `General Statistics` table, but in a simpler, tabular format that is more convenient for comparisons. It looks like this:  
 
 ```
 |ID                                  |    Dups| GC|   Seqs| Error rate| Non-primary| Reads mapped| % Mapped| Total seqs|