obsexp upgrade

README.md

@@ -4,6 +4,8 @@ Ready to use Nextflow CGI workflow available on genotoul /work/project/lpgp/Next
 
 ## Usage example
 
+### newcpgreport
+
 ```bash
 #!/bin/bash
 #SBATCH -J CGI
@@ -23,6 +25,37 @@ nextflow run /work/project/lpgp/Nextflow/cgi/ \
 --out_dir "${PWD}/results"
 ```
 
+### cpg_lh (UCSC)
+
+```bash
+#!/bin/bash
+#SBATCH -J CGI
+#SBATCH -p unlimitq
+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" \
+--cpglh \
+--out_dir "${PWD}/results"
+```
+
+### CpG Obs/Exp window
+
+```bash
+#!/bin/bash
+#SBATCH -J CGI
+#SBATCH -p unlimitq
+module load system/singularity-3.7.3
+module load bioinfo/Nextflow-v21.04.1
+nextflow run /work/project/lpgp/Nextflow/cgi/ \
+-profile slurm \
+--genome "genome.fa.gz" \
+--obsexp \
+--obsexp_w 200 \
+--out_dir "${PWD}/results"
+```
+
 ## Install CGI flow and build singularity image
 
 Clone CGI git and build local singularity image (with system admin) based on the provided singularity definition file.

bin/ObsExp.R

@@ -155,7 +155,15 @@ Data[,query:=NULL]
 # write
 data.table::fwrite(
     Data,
-    file="ObsExp_w.txt",
+    file=paste(
+        sub(
+            " .+$",
+            "",
+            names(Fa)
+        ),
+        "ObsExp_w.txt",
+        sep ="_"
+    ),
     sep="\t",
     quote=FALSE,
     col.names = FALSE
@@ -163,6 +171,9 @@ data.table::fwrite(
 
 # gzip
 R.utils::gzip(
-    "ObsExp_w.txt"
+    list.files(
+        pattern="ObsExp_w.txt",
+        full.names = TRUE
+    )
 )
 #//
\ No newline at end of file

modules/modules.nf

@@ -117,10 +117,7 @@ process OBSEXP_COLLECT {
 	script:
 	"""
 	echo -e "seqnames\\tstart\\tend\\width\\tC\\tG\\tCpG\\tObsExp" > "ObsExp_w${params.obsexp_w}.txt"
-	cat ./*.gz >> "ObsExp_w${params.obsexp_w}.txt"
+	zcat ./*.gz >> "ObsExp_w${params.obsexp_w}.txt"
 	gzip "ObsExp_w${params.obsexp_w}.txt"
 	"""
-}
-
-
-
+}
\ No newline at end of file