added more information for internal usage

README.md

@@ -2,6 +2,21 @@
 
 ## Install
 
+### Dependencies
+
+  - {+ nextflow +}
+  - samtools
+  - bedtools
+  - bwa
+  - minimap2
+  - qualimap
+  - multiqc
+  - r-base
+  - r-ggplot2
+  - r-dplyr
+
+### Installation with conda
+
 ```
 conda env create -f environment.yml
 conda activate backmap
@@ -111,7 +126,12 @@ $ nextflow run backmap.nf --assembly assembly.fasta --pacbio-bam-files-- pacbio1
 
 R scripts have been improved and rewritten.
 
+#### R All plot perl
+
 ![R All plot from the original perl pipeline][oldRall]
+
+#### R All plot perl
+
 ![R All plot from the new nextflow pipeline][newRall]
 
 ### Resolved bugs of the perl pipeline
@@ -123,7 +143,7 @@ While running the original pipeline with different kinds of parameters, some bug
 | 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 |
 
-## Test
+## Development/Test
 
 ### Install dev/test environments
 
@@ -131,28 +151,89 @@ While running the original pipeline with different kinds of parameters, some bug
 
 The development environment includes everything, which is needed for running the original perl pipeline, the newly created nextflow pipeline, and the snakemake test pipeline
 
+```yaml
+---
+name: backmap-development
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - snakemake
+  - mamba
+  - nextflow
+  - perl
+  - perl-app-cpanminus
+  - samtools
+  - bedtools
+  - bwa
+  - minimap2
+  - qualimap
+  - multiqc
+  - r-base
+  - r-ggplot2
+  - r-dplyr
 ```
-# 
 
-```
+Perl packages needed for original workflow
+
+ - Cwd
+ - IPC::Cmd
+ - Number::FormatEng
+ - Parallel::Loops
 
 ```
+# create and activate conda environment
 conda env create -f environment-dev.yml
-conda activate backmap-dev
+conda activate backmap-development
+# install perl packages and check if they are really available
+env PERL5LIB="" PERL_LOCAL_LIB_ROOT="" PERL_MM_OPT="" PERL_MB_OPT="" cpanm Cwd IPC::Cmd Number::FormatEng Parallel::Loops
+for i in Cwd IPC::Cmd Number::FormatEng Parallel::Loops;
+do
+  perl -M"$i" -e 'print "Modul exists\\n";'
+done
 ```
 
-#### Test
+#### Testing with Snakemake pipeline
+
+##### Install
+
+```yaml
+name: backmap-test
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - snakemake
+  - mamba
+```
+
+##### Prepare Test environments
 
 ```
+# create and activate conda environment
 conda env create -f environment-test.yml
 conda activate backmap-test
+# create environments for all jobs
 snakemake --profile sm_profile/ --conda-create-envs-only -F
+# install perl packages
 snakemake --profile sm_profile/ -f install_perl_packages
+```
+
+##### Run all tests
+
+```
 snakemake --profile sm_profile/ -F 
 ```
 
+#### Linter
+
+TODO
 
-# original perl script
+----------------------------------------
+
+# Original perl script
 
 https://github.com/schellt/backmap
 
@@ -176,13 +257,46 @@ 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/>
 
+--------------------------------------------------------------------------------------
+
 # Internal notes
 
-There are no Nanopore reads.
+## Directory
+
+`/vol/cb/projects/112020_tbg_backmap`
+
+## Directory structure
+
+## Test files
+
+The dataset for testing was brought to us via JLUBox and is now stored at
+`/vol/cb/projects/112020_tbg_backmap/dataset1/Test_datasets.zip`
+
+```
+-r--r--r--  1 rmueller cb  16G Dec  1 15:13 Test_datasets.zip
+```
+
+### Content
+```
+Archive:  Test_datasets.zip
+  Length      Date    Time    Name
+---------  ---------- -----   ----
+2209018648  2020-08-26 14:16   dgal_1.paired.confilter.fq.gz
+2375279937  2020-08-26 14:14   dgal_2.paired.confilter.fq.gz
+ 38668802  2020-08-26 14:14   dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta.gz
+1659448324  2020-08-26 14:10   pacbio_gal.target-and-other.blobfilter.fastq.gz
+473770619  2020-08-26 14:11   dgal.confilter.fq.gz
+2760385779  2020-08-26 14:09   dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta.pb.sort.bam
+6667551038  2020-08-26 14:13   dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta.sort.bam
+---------                     -------
+16184123147                     7 files
+```
+
+There are no Nanopore reads. The snakemake pipeline simulates them
 
-| what | file |
+| Purpose | File |
 | ---- | ---- |
-| genome assembly | dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta.gz |
+| Genome assembly | dgal_ra_pb-target-and-other_ill-confilter.blobfilter.rmmt_sspace-lr3_lrgc3_pg3_pilon_3.fasta.gz |
 | Illumina forward reads | dgal_1.paired.confilter.fq.gz | 
 | Illumina reverse reads | dgal_2.paired.confilter.fq.gz | 
 | Illumina unpaired reads | dgal.confilter.fq.gz |