--- a/README.md	Thu Aug 08 07:40:36 2019 -0400
+++ b/README.md	Thu Feb 25 13:36:15 2021 +0000
@@ -1,123 +1,123 @@
-# ARGalaxy Immune Repertoire
-This is the GitHub repository for the ARGalaxy Immune repertoire pipeline.  
-The Galaxy tool version can be found [here](https://toolshed.g2.bx.psu.edu/repository/browse_repositories_i_own?sort=name&operation=view_or_manage_repository&id=2e457d63170a4b1c).  
-The docker version can be found [here](https://github.com/ErasmusMC-Bioinformatics/ARGalaxy-docker).
-
-## Overview
-
-In execution order:
-
-#### imgt_loader or igblast
-
-###### imgt_loader (Recommended)
-Start the analysis with [IMGT HighV Quest](https://www.imgt.org/HighV-QUEST/) archives.  
-An IMGT archive file holds [multiple tabular files](http://www.imgt.org/IMGT_vquest/share/textes/imgtvquest.html#output3), this script extracts the specific columns relevant to the analysis from several of these files.
-
-`Rscript imgt_loader.r 1_Summary.txt 3_Nt-sequences.txt 5_AA-sequences.txt 6_Junction.txt 4_IMGT-gapped-AA-sequences.txt /path/to/output.txt`
-
-
-###### igblast
-Start the analysis with FASTA files that are aligned with [igblast](https://www.ncbi.nlm.nih.gov/igblast/).  
-Note that this method will provide less information than the IMGT archive.
-
-`sh igblast.sh /path/to/sequences.fasta species locus /path/to/output.txt`
-
-#### experimental_design
-This script will merge multiple result files (from the last step) into a single file with an additional ID and Replicate column to differentiate the individual samples during the analysis and to allow for analysis across samples.
-
-`Rscript experimental_design.r /path/to/input_1 id_1 [/path/to/input_2 id_2] [/path/to/input_n id_n] /path/to/output`
-
-#### report_clonality
-The R script that creates the analysis result.
-
-`sh r_wrapper.sh /path/to/experimental_design/output.txt /path/to/output_dir/output.html /path/to/output_dir "clonaltype" "species" "locus" "filter_productive" "clonality_method"`  
-
-###### parameters
-Clonaltype:  
-- none
-- Top.V.Gene,CDR3.Seq
-- Top.V.Gene,CDR3.Seq.DNA
-- Top.V.Gene,Top.J.Gene,CDR3.Seq
-- Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA
-- Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA
-
-Species:
-- Homo sapiens functional
-- Homo sapiens
-- Homo sapiens non-functional
-- Bos taurus
-- Bos taurus functional
-- Bos taurus non-functional
-- Camelus dromedarius
-- Camelus dromedarius functional
-- Camelus dromedarius non-functional
-- Canis lupus familiaris
-- Canis lupus familiaris functional
-- Canis lupus familiaris non-functional
-- Danio rerio
-- Danio rerio functional
-- Danio rerio non-functional
-- Macaca mulatta
-- Macaca mulatta functional
-- Macaca mulatta non-functional
-- Mus musculus
-- Mus musculus functional
-- Mus musculus non-functional
-- Mus spretus
-- Mus spretus functional
-- Mus spretus non-functional
-- Oncorhynchus mykiss
-- Oncorhynchus mykiss functional
-- Oncorhynchus mykiss non-functional
-- Ornithorhynchus anatinus
-- Ornithorhynchus anatinus functional
-- Ornithorhynchus anatinus non-functional
-- Oryctolagus cuniculus
-- Oryctolagus cuniculus functional
-- Oryctolagus cuniculus non-functional
-- Rattus norvegicus
-- Rattus norvegicus functional
-- Rattus norvegicus non-functional
-- Sus scrofa
-- Sus scrofa functional
-- Sus scrofa non-functional
-
-Locus:
-- TRA
-- TRD
-- TRG
-- TRB
-- IGH
-- IGI
-- IGK
-- IGL
-
-Filter productive:
-- yes
-- no
-
-Clonality Method:
-- none
-- old
-- boyd
-
-## complete.sh
-This script will run all of the above for you, it will detect if you are using FASTA files or IMGT archives and use the appropriate tools.
-
-`sh complete.sh /path/to/input_1 id_1 [/path/to/input_n id_n] /path/to/out_dir/out.html /path/to/out_dir clonaltype species locus filter_productive clonality_method`  
-See "report_clonality" for the parameter options.
-
-## Dependencies
-- Linux
-- R
-  - gridExtra
-  - ggplot2
-  - plyr
-  - data.table
-  - reshape2
-  - lymphclon
-
-#### optional
-- Circos
-- IgBlast
-- igblastwrp
+# ARGalaxy Immune Repertoire
+This is the GitHub repository for the ARGalaxy Immune repertoire pipeline.  
+The Galaxy tool version can be found [here](https://toolshed.g2.bx.psu.edu/repository/browse_repositories_i_own?sort=name&operation=view_or_manage_repository&id=2e457d63170a4b1c).  
+The docker version can be found [here](https://github.com/ErasmusMC-Bioinformatics/ARGalaxy-docker).
+
+## Overview
+
+In execution order:
+
+#### imgt_loader or igblast
+
+###### imgt_loader (Recommended)
+Start the analysis with [IMGT HighV Quest](https://www.imgt.org/HighV-QUEST/) archives.  
+An IMGT archive file holds [multiple tabular files](http://www.imgt.org/IMGT_vquest/share/textes/imgtvquest.html#output3), this script extracts the specific columns relevant to the analysis from several of these files.
+
+`Rscript imgt_loader.r 1_Summary.txt 3_Nt-sequences.txt 5_AA-sequences.txt 6_Junction.txt 4_IMGT-gapped-AA-sequences.txt /path/to/output.txt`
+
+
+###### igblast
+Start the analysis with FASTA files that are aligned with [igblast](https://www.ncbi.nlm.nih.gov/igblast/).  
+Note that this method will provide less information than the IMGT archive.
+
+`sh igblast.sh /path/to/sequences.fasta species locus /path/to/output.txt`
+
+#### experimental_design
+This script will merge multiple result files (from the last step) into a single file with an additional ID and Replicate column to differentiate the individual samples during the analysis and to allow for analysis across samples.
+
+`Rscript experimental_design.r /path/to/input_1 id_1 [/path/to/input_2 id_2] [/path/to/input_n id_n] /path/to/output`
+
+#### report_clonality
+The R script that creates the analysis result.
+
+`sh r_wrapper.sh /path/to/experimental_design/output.txt /path/to/output_dir/output.html /path/to/output_dir "clonaltype" "species" "locus" "filter_productive" "clonality_method"`  
+
+###### parameters
+Clonaltype:  
+- none
+- Top.V.Gene,CDR3.Seq
+- Top.V.Gene,CDR3.Seq.DNA
+- Top.V.Gene,Top.J.Gene,CDR3.Seq
+- Top.V.Gene,Top.J.Gene,CDR3.Seq.DNA
+- Top.V.Gene,Top.D.Gene,Top.J.Gene,CDR3.Seq.DNA
+
+Species:
+- Homo sapiens functional
+- Homo sapiens
+- Homo sapiens non-functional
+- Bos taurus
+- Bos taurus functional
+- Bos taurus non-functional
+- Camelus dromedarius
+- Camelus dromedarius functional
+- Camelus dromedarius non-functional
+- Canis lupus familiaris
+- Canis lupus familiaris functional
+- Canis lupus familiaris non-functional
+- Danio rerio
+- Danio rerio functional
+- Danio rerio non-functional
+- Macaca mulatta
+- Macaca mulatta functional
+- Macaca mulatta non-functional
+- Mus musculus
+- Mus musculus functional
+- Mus musculus non-functional
+- Mus spretus
+- Mus spretus functional
+- Mus spretus non-functional
+- Oncorhynchus mykiss
+- Oncorhynchus mykiss functional
+- Oncorhynchus mykiss non-functional
+- Ornithorhynchus anatinus
+- Ornithorhynchus anatinus functional
+- Ornithorhynchus anatinus non-functional
+- Oryctolagus cuniculus
+- Oryctolagus cuniculus functional
+- Oryctolagus cuniculus non-functional
+- Rattus norvegicus
+- Rattus norvegicus functional
+- Rattus norvegicus non-functional
+- Sus scrofa
+- Sus scrofa functional
+- Sus scrofa non-functional
+
+Locus:
+- TRA
+- TRD
+- TRG
+- TRB
+- IGH
+- IGI
+- IGK
+- IGL
+
+Filter productive:
+- yes
+- no
+
+Clonality Method:
+- none
+- old
+- boyd
+
+## complete.sh
+This script will run all of the above for you, it will detect if you are using FASTA files or IMGT archives and use the appropriate tools.
+
+`sh complete.sh /path/to/input_1 id_1 [/path/to/input_n id_n] /path/to/out_dir/out.html /path/to/out_dir clonaltype species locus filter_productive clonality_method`  
+See "report_clonality" for the parameter options.
+
+## Dependencies
+- Linux
+- R
+  - gridExtra
+  - ggplot2
+  - plyr
+  - data.table
+  - reshape2
+  - lymphclon
+
+#### optional
+- Circos
+- IgBlast
+- igblastwrp