readme update

README.md

@@ -15,7 +15,17 @@ git clone https://forgemia.inra.fr/lpgp/cgi.git
 sudo singularity build ./cgi/singularity/CGI.sif ./cgi/singularity/CGI.def
 ```
 
-## Usage example ENBOSS newcpgreport
+## Usage example
+
+design.csv file must have *ID* and *target* header and write with comma separator.
+
+|ID|target|
+|:-|:-|
+|A|/path/to/targetA.fa.gz|
+|B|/path/to/targetB..fa.gz|
+|C|/path/to/targetC.fa.gz|
+
+###  ENBOSS newcpgreport
 
 ```bash
 #!/bin/bash
@@ -26,7 +36,7 @@ module load system/singularity-3.7.3
 module load bioinfo/Nextflow-v21.04.1
 nextflow run /work/project/lpgp/Nextflow/cgi/ \
 -profile slurm \
---genome "genome.fa.gz" \
+--input "design.csv" \
 --newcpgreport \
 --window 100 \
 --shift 1 \
@@ -37,7 +47,7 @@ nextflow run /work/project/lpgp/Nextflow/cgi/ \
 --out_dir "${PWD}/results"
 ```
 
-## Usage example UCSC cpg_lh
+### UCSC cpg_lh
 
 ```bash
 #!/bin/bash
@@ -48,12 +58,12 @@ module load system/singularity-3.7.3
 module load bioinfo/Nextflow-v21.04.1
 nextflow run /work/project/lpgp/Nextflow/cgi/ \
 -profile slurm \
---genome "genome.fa.gz" \
+--input "design.csv" \
 --cpglh \
 --out_dir "${PWD}/results"
 ```
 
-## Usage example CpG Obs/Exp slinding windows
+### CpG Obs/Exp sliding windows
 
 ```bash
 #!/bin/bash
@@ -64,7 +74,7 @@ module load system/singularity-3.7.3
 module load bioinfo/Nextflow-v21.04.1
 nextflow run /work/project/lpgp/Nextflow/cgi/ \
 -profile slurm \
---genome "genome.fa.gz" \
+--input "design.csv" \
 --obsexp \
 --obsexp_shift 200 \
 --obsexp_window 200 \
@@ -76,8 +86,8 @@ nextflow run /work/project/lpgp/Nextflow/cgi/ \
 Please refer to [EMBOSS newcpgreport](https://www.bioinformatics.nl/cgi-bin/emboss/help/newcpgreport), and [UCSC cpg_lh](http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1136815349_vADDCkvwSdu3g8CimOykIvSHZHar&db=rn3&c=chr5&g=cpgIsland) for complete arguments explanation.
 
 ```bash
-# genome input
-genome = false
+# sequences input
+input = false
 
 # newcpgreport options
 newcpgreport = false