readme update

README.md

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 snakemake obitools workflow to process rapidrun eDNA data
 
 
-
-# Prerequisites
-
-
-* python3
-
-* snakemake
-
-* singularity
-
-python3 dependencies
-
-```
-pip3 install pandas
-pip3 install biopython
-```
-
-python3 dependencies to run `snakemake`:
-
-```
-pip3 install datrie
-pip3 install ConfigArgParse
-pip3 install appdirs
-pip3 install gitdb2
-```
-
-# Configuration / input files
-
-You have to set 2 files:
-
-* `RAPIDRUN_METADATA` *e.g.* [all_samples.tsv](resources/test/all_samples.tsv)
-* `CONFIG_FILE` *e.g.* [config/config.yaml](config/)
-
-
-# The Workflow
-
-## 1. Set rapidrun 
-
-Indicate the absolute path of rapidrun metadata table [all_samples.tsv](resources/test/all_samples.tsv) in the `fichiers` `rapidrun` field in [config/config.yaml](config/)
-
-
-```
-cd 01_settings
-snakemake --configfile "../"$CONFIGFILE -s readwrite_rapidrun_demultiplexing.py --cores $CORES
-cd ..
-```
-This command will read `CONFIGFILE` and the `RAPIDRUN_METADATA` then return a file [results/01_settings/all_demultiplex.csv](results/01_settings/) which can be used to process rapidrun data in the next steps of the workflow.
-
-[results/01_settings/all_demultiplex.csv](results/01_settings/) has 14 fields : *demultiplex,projet,marker,run,plaque,sample,barcode5,barcode3,primer5,primer3,min_f,min_r,lenBarcode5,lenBarcode3* and each row is an unique sample which belong to an unique marker and a project.
-
-## 2 Assembly
-
-```
-cd 02_assembly
-snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
-cd ..
-```
-
-Merge paired-end sequences and remove unaligned sequences records. Results are stored into [results/02_assembly](results/02_assembly)
-
-## 3 Demultiplexing
-
-```
-cd 03_demultiplex
-snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
-cd ..
-```
-
-The tags correspond to short and specific sequences added on the 5’ end of each primer to distinguish the different samples.
-Check results of demultiplexing into [results/03_demultiplex](results/03_demultiplex)
-
-## 4 Filter samples
-
-```
-cd 04_filter_samples
-snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
-cd ..
-```
-
-For each sample, dereplicate sequences, remove sequences with a given length, remove sequences with IUAPC ambiguity, remove PCR clone, remove sequences which are classified as 'internal' by `obiclean`
-
-Check results into [results/04_filter_samples](results/04_filter_samples)
-
-## 5 Concatenate samples into runs
-
-```
-for projet in `ls results/04_filter_samples/04_filtered/`;
-do 
- for marker in `ls results/04_filter_samples/04_filtered/${projet}/`;
- do
-  for run in `ls results/04_filter_samples/04_filtered/${projet}/${marker}/`;
-  do
-  echo results/04_filter_samples/04_filtered/${projet}/${marker}/${run};
-  mkdir -p results/05_assignment/01_runs/${projet}/${marker}/
-  cat results/04_filter_samples/04_filtered/${projet}/${marker}/${run}/*.c.r.l.u.fasta > results/05_assignment/01_runs/${projet}/${marker}/${run}.fasta
-  done
- done
-done
-```
-
-sample files are concatenated by run into [results/05_assignment/01_runs](results/05_assignment/01_runs)
-
-## 6 Assignment
-
-```
-cd 05_assignment
-snakemake --configfile "../"$CONFIGFILE -s Snakefile --cores $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk --home $HOME" --latency-wait 20
-cd ..
-```
-
-Assign each sequence to a taxon. Format the output into a csv results in folder [results/06_final_tables](results/06_final_tables)
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+Visit project [wiki](https://gitlab.mbb.univ-montp2.fr/edna/snakemake_rapidrun_obitools/-/wikis/home) for documentation.
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