Commit a4fec821 authored by peguerin's avatar peguerin
Browse files

readme update

parent 22a20c30
......@@ -6,23 +6,27 @@ OTU clustering with SWARM on RAPIDRUN data encapsulated in SNAKEMAKE
# Prerequisites
python3
* python3
pandas
biopython
* snakemake
* singularity
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
......@@ -38,4 +42,91 @@ You have to set 2 files:
CORES=32
CONFIGFILE="../01_infos/config_test.yaml"
bash main.sh $CORES $CONFIGFILE
```
\ No newline at end of file
```
# Run from scratch
## clone repositories
```
git clone git@gitlab.mbb.univ-montp2.fr:edna/snakemake_rapidrun_swarm.git
cd snakemake_rapidrun_swarm
```
## write demultiplexing table
From
- `01_infos/config_test.yaml`
* `fichiers:` `rapidrun`
* `fichiers:` `dat`
:warning: the colon "marker" into `fichiers:` `rapidrun` must be the same name as marker's keys of `fichiers:` `dat` into `01_infos/config_test.yaml`
This will generate a file `01_infos/all_demultiplex.csv` with each line arguments for command.
```
snakemake --configfile 01_infos/config_test.yaml -s readwrite_rapidrun_demultiplexing.py
```
## merge fastq
From
- `01_infos/config_test.yaml`
* `fichiers:` `rapidrun`
Deduce the `{run}` fastq paired-end to merge
:warning: guadeloupe have been removed by hand into 02_assembly/Snakefile !!!
```
cd 02_assembly
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd ..
```
## demultiplexing
From
- `01_infos/config_test.yaml`
* `fichiers:` `rapidrun`
will generate demultiplexed .fasta and .qual files for each `{projet}`/`{marker}`/`{sample}` into `03_demultiplexing`
```
cd 03_demultiplexing
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd ..
```
## cat qualities
From
- `01_infos/config_test.yaml`
* `fichiers:` `rapidrun`
Simply concatenate and format .qual files by `{projet}`/`{marker}`
```
cd 04_cat_quality
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd ..
```
## clustering
```
cd 05_clustering
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
cd ..
```
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