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edna
snakemake_rapidrun_swarm
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a4fec821
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a4fec821
authored
Feb 05, 2020
by
peguerin
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readme update
parent
22a20c30
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README.md
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@@ -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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