rewrite README and add pdfs

README.md

-# (new) Nextflow pipeline
+# Backmap Nextflow pipeline
 
 ## Install
 
 ```
 conda env create -f environment.yml
-
 conda activate backmap
 ```
 
@@ -58,7 +57,7 @@ Optional Options: [default]
                                                         Will be created if not existing
                 --prefix                        STR     Prefix of output files
                 --keep-temporary                        Keep temporary, intermediate files [false]
-                --threads       INT                     Maximum number of threads per process [1]
+                --threads                       INT     Maximum number of threads per process [1]
                                                         This is not the total number of available threads!
 
                 --skip-quality-control                  Skip qualimap bamqc run [false]
@@ -79,55 +78,79 @@ Optional Options: [default]
 
 ```
 
-## Test
+## Changes to the original perl pipeline
 
-### Install dev/test environments
+### Parameters
 
-#### Development
+ - {+ all options now have a long version, short version is currently not available +}
+ - {+ added option `--illumina-bam-files`, `--pacbio-bam-files`, `--nanopore-bam-files`, which substitute `-b` +}
+ - {+ `--debug` prints internal variables for faster development and bug investigations +}
+ - {+ `--threads` sets the maximum number of threads per process (not maximum number of threads of the whole workflow) +}
+ - {- removed `-b`:splitted into three different options -}
+ - {- removed `-sort`: every bam is now sorted -}
+ - {- removed `-v`: removed, because this is a nextflow feature -}
+ - {- removed `-dry-run` -}
+ - {- removed `-t`: handled by nextflow -}
+
+### Multiple files of one kind
 
+Multiple files of one kind, e.g., three different PacBio runs, are now given as one string with each run comma separated instead of giving one parameter multiple times.
 ```
-conda env create -f environment-dev.yml
-conda activate backmap-dev
+$ nextflow run backmap.nf --assembly assembly.fasta --pacbio pacbio1.fq,pacbio2.fq,pacbio3.fq
 ```
 
-#### Snakemake
+### Genome size estimation with bam files
+
+Genome size estimation with bam files can now be done if assembly is given
 
 ```
-conda env create -f environment-test.yml
-conda activate backmap-test
-snakemake --profile sm_profile/ --conda-create-envs-only -F
-snakemake --profile sm_profile/ -f install_perl_packages
-snakemake --profile sm_profile/ -F 
+$ nextflow run backmap.nf --assembly assembly.fasta --pacbio-bam-files-- pacbio1.bam,pacbio2.bam,pacbio3.bam
 ```
 
-## What's new? What did change?
+### Improved R scripts
 
-### new options
+R scripts have been improved and rewritten.
 
-1. all options now have a long version, short version is currently not available
-1. `--illumina-bam-files`, `--pacbio-bam-files`, `--nanopore-bam-files` instead of `-b`
-1. `--debug` prints internal variables for faster development and bug investigations
-1. `--threads` sets the maximum number of threads per process (not maximum number of threads of the whole workflow)
+![R All plot from the original perl pipeline][oldRall]
+![R All plot from the new nextflow pipeline][newRall]
 
-### options not available anymore
+### Resolved bugs of the perl pipeline
 
-1. `-b` -> splitted into three different options
-1. `-sort` -> every bam is now sorted
-1. `-v` -> removed, because this is a nextflow feature
-1. `-dry-run` -> removed
-1. `-t` -> removed, because this is handled by nextflow
+While running the original pipeline with different kinds of parameters, some bugs appeared
+|                              Issue                              | Solved? |                      PR                   |
+| --------------------------------------------------------------- | ------- | ------------------------------------------|
+| keep temporary option did not work properly                     |   yes   | https://github.com/schellt/backmap/pull/1 |
+| plot all did not work, if illumina reads were not present       |   yes   | https://github.com/schellt/backmap/pull/5 |
+| pipeline crashed on rerun due to not enforcing symlink creation |   yes   | https://github.com/schellt/backmap/pull/4 |
 
-### multifile call
+## Test
 
-Multi files of one kind, e.g., three different pacbio runs, are now given as one string with each run comma separated instead of giving one parameter multiple times.
+### Install dev/test environments
 
-### Genome size estimation with bam files
+#### Development
 
-Genome size estimation with bam files can now be done if assembly is given
+The development environment includes everything, which is needed for running the original perl pipeline, the newly created nextflow pipeline, and the snakemake test pipeline
 
-### Improved R scripts
+```
+# 
+
+```
+
+```
+conda env create -f environment-dev.yml
+conda activate backmap-dev
+```
+
+#### Test
+
+```
+conda env create -f environment-test.yml
+conda activate backmap-test
+snakemake --profile sm_profile/ --conda-create-envs-only -F
+snakemake --profile sm_profile/ -f install_perl_packages
+snakemake --profile sm_profile/ -F 
+```
 
-R scripts have been improved and rewritten
 
 # original perl script
 
@@ -153,7 +176,7 @@ Quinlan AR, Hall IM (2010). BEDTools: a flexible suite of utilities for comparin
 - Rscript:  
 R Core Team (2019). R: A Language and Environment for Statistical Computing. <http://www.R-project.org/>
 
-# testdata
+# Internal notes
 
 There are no Nanopore reads.
 
@@ -166,3 +189,6 @@ There are no Nanopore reads.
 | PacBio reads | pacbio_gal.target-and-other.blobfilter.fastq.gz | 
 | Illumina mapping | dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta.sort.bam | 
 | PacBio mapping | dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta.pb.sort.bam | 
+
+[oldRall]: img/RallOld.pdf
+[newRall]: img/RallNew.pdf