Enhance docker (#121)

* start use docker script * use pip script than src dir * add local/Lifebit support compatibility
LabShengLi · Oct 25, 2021 · 0555898 · 0555898
1 parent 7773f74
commit 0555898
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Showing 16 changed files with 106 additions and 108 deletions.
diff --git a/README.md b/README.md
@@ -25,7 +25,7 @@
 * Enables users to process **terabasescale** Oxford Nanopore sequencing datasets.
 * Provide a one command line, **end-to-end pipeline** for analyzing Nanopore sequencing data for all methylation-calling tools.
 * Support **various platform** executions: local, HPC and CloudOS, **without needs for tools' installation** (NANOME support docker and singularity).
-* **First standardized whole genome-wide evaluation framework**, considering per-read and per-site performance for singletons/non-singletons, genic and intergenic regions, CpG islands/shores/shelves, differenct CG densities regions and repetitive regions. 
+* **First standardized whole genome-wide evaluation framework**, considering per-read and per-site performance for singletons/non-singletons, genic and intergenic regions, CpG islands/shores/shelves, different CG densities regions and repetitive regions. 
 * The **first Nextflow based DNA methylation-calling pipeline**. Please check more articles about Nextflow based workflow technology from Nature Biotechnology: https://doi.org/10.1038/s41587-020-0439-x and https://doi.org/10.1038/nbt.3820.
 
 ### CI/CD features

diff --git a/conf/executors/lifebit.config b/conf/executors/lifebit.config
@@ -11,6 +11,8 @@ params{
     input = 'https://github.com/TheJacksonLaboratory/nanome/raw/master/test_data/human_ci_test_fast5.tar.gz'
 	reference_genome = 'https://zenodo.org/record/5513090/files/hg38_chr22.tar.gz'
 
+	outputDir = 'results'
+
  	useDeepModCluster = false
     moveOption = true
 	chrSet = true

diff --git a/conf/executors/local.config b/conf/executors/local.config
@@ -1,9 +1,10 @@
-docker.enabled = true
-
-params {
-    executor = 'local'
-}
-
+/*
+ * -------------------------------------------------
+ *  Nextflow config for running on Local
+ * -------------------------------------------------
+ * Defines bundled configurations for process running
+ * on Local
+ */
 process {
-    container = params.docker_name
+    executor = 'local'
 }
diff --git a/demo_google_cloud.sh b/demo_google_cloud.sh
@@ -35,6 +35,7 @@ nextflow run main.nf\
 
 echo "### nanome pipeline for demo data on google DONE"
 
+exit 0
 ###########################################
 ###########################################
 ###########################################

diff --git a/demo_hpc_winter.sh b/demo_hpc_winter.sh
@@ -27,11 +27,12 @@ rm -rf ${workDir} ${outputsDir}
 ########################################
 # Running pipeline for demo human data
 # More options: -with-report -with-timeline -with-trace -resume -with-dag nanome_dag.png
-#     -config conf/executors/jaxhpc_input.config\
+#
 module load singularity
-set -x
+set -ex
 nextflow run main.nf\
     -profile singularity,hpc\
+    -config conf/executors/jaxhpc_input.config\
     -work-dir ${workDir}\
     --outputDir ${outputsDir}\
     --dsname TestData\

diff --git a/docs/Eval.md b/docs/Eval.md
@@ -24,8 +24,6 @@ The script `read_level_eval.py` is desinged for general purpose of read-level pe
 
 ```angular2html
 read_level_eval.py -v
-
-read_level_eval (NANOME) v1.3.7
 ```
 
 ## Sample usage
@@ -130,8 +128,6 @@ The script `site_level_eval.py` is desinged for general purpose of site-level pe
 
 ```angular2html
 site_level_eval.py -v
-
-site_level_eval (NANOME) v1.3.7
 ```
 
 
@@ -236,8 +232,6 @@ The script `tss_eval.py` is desinged for general purpose of converting raw resul
 
 ```angular2html
 tss_eval.py -v
-
-tss_eval (NANOME) v1.3.7
 ```
 
 ## Sample usage for read-level format unification

diff --git a/ecoli_hpc_winter.sh b/ecoli_hpc_winter.sh
@@ -8,7 +8,8 @@
 #SBATCH --mem=20G # memory pool for all cores
 #SBATCH --time=02:00:00 # time
 #SBATCH --output=log/%x.%j.log # STDOUT & STDERR
-
+#SBATCH [email protected]
+#SBATCH --mail-type=END
 date; hostname; pwd
 
 # Base directory of running and output for nanome
@@ -26,12 +27,12 @@ rm -rf ${workDir} ${outputsDir}
 ########################################
 # Running pipeline for E. coli data
 module load singularity
-set -x
+set -ex
 nextflow run main.nf\
     -profile singularity,hpc\
+    -config conf/executors/jaxhpc_input.config,conf/examples/ecoli_demo.config\
     -work-dir ${workDir}\
     --outputDir ${outputsDir}\
-    -config conf/executors/jaxhpc_input.config,conf/examples/ecoli_demo.config\
     --cleanCache false
 
 # Report