Commit 0c3b5fef authored by peguerin's avatar peguerin
Browse files

readme update

parent f051cb77
......@@ -40,7 +40,7 @@ You have to set 2 files:
```
CORES=32
CONFIGFILE="../01_infos/config_test.yaml"
CONFIGFILE="01_infos/config_test.yaml"
bash main.sh $CORES $CONFIGFILE
```
......@@ -62,9 +62,9 @@ From
* `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`
* :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.
* This will generate a file `01_infos/all_demultiplex.csv` with each line arguments for each command to run in parallel.
```
snakemake --configfile 01_infos/config_test.yaml -s readwrite_rapidrun_demultiplexing.py
......@@ -77,9 +77,9 @@ From
- `01_infos/config_test.yaml`
* `fichiers:` `rapidrun`
Deduce the `{run}` fastq paired-end to merge
* Deduce the `{run}` fastq paired-end to merge
:warning: guadeloupe have been removed by hand into 02_assembly/Snakefile !!!
* :warning: guadeloupe have been removed by hand into [02_assembly/Snakefile](02_assembly/Snakefile) !!!
```
......@@ -94,7 +94,7 @@ From
- `01_infos/config_test.yaml`
* `fichiers:` `rapidrun`
will generate demultiplexed .fasta and .qual files for each `{projet}`/`{marker}`/`{sample}` into `03_demultiplexing`
* will generate demultiplexed .fasta for each `{projet}`/`{marker}`/`{sample}` into `03_demultiplexing`
```
......@@ -109,7 +109,7 @@ From
- `01_infos/config_test.yaml`
* `fichiers:` `rapidrun`
Simply concatenate and format .qual files by `{projet}`/`{marker}`
* will concatenate and format .qual files by `{projet}`/`{marker}`
```
cd 04_cat_quality
......@@ -119,6 +119,8 @@ cd ..
## clustering
...
```
cd 05_clustering
snakemake --configfile $CONFIGFILE -s Snakefile -j $CORES --use-singularity --singularity-args "--bind /media/superdisk:/media/superdisk" --latency-wait 20
......
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