start making the new wipertools repo

.devcontainer/Dockerfile

@@ -0,0 +1,40 @@
+FROM condaforge/mambaforge
+LABEL maintainer="mazza.tommaso@gmail.com"
+
+# ENV bbmap_version 39.08
+# ENV PATH "$PATH:/tmp/jre1.8.0_161/bin/"
+
+# RUN mamba config --set channel_priority strict
+RUN mamba install python=3.12
+# RUN mamba install -c conda-forge -c bioconda snakemake -y
+# RUN mamba install -c bioconda trimmomatic -y
+
+# Install fastqwiper from conda
+# RUN mamba install -y -c bfxcss -c conda-forge fastqwiper
+
+# Install gzrt, BBmap, and Java
+# RUN apt update
+# RUN apt-get install gzrt -y
+# ADD https://sourceforge.net/projects/bbmap/files/BBMap_${bbmap_version}.tar.gz/download /fastqwiper/BBMap_${bbmap_version}.tar.gz
+# RUN cd fastqwiper &&\
+#     tar -xvzf BBMap_${bbmap_version}.tar.gz &&\
+#     rm BBMap_${bbmap_version}.tar.gz 
+# ADD http://javadl.oracle.com/webapps/download/AutoDL?BundleId=230532_2f38c3b165be4555a1fa6e98c45e0808 /tmp/java.tar.gz
+# RUN cd /tmp/ &&\
+# 	tar xvzf java.tar.gz
+
+WORKDIR /fastqwiper
+
+# COPY pipeline pipeline
+# COPY run_wiping.sh run_wiping.sh
+COPY data data
+# RUN chmod +x run_wiping.sh
+
+
+# ENTRYPOINT ["/fastqwiper/run_wiping.sh"]
+# # paired mode, 4 cores, sample name, ASCII offset (33=Sanger, 64=old Solexa), alphabet (e.g., ACGTN), log frequency (500000)
+# CMD ["paired", "4", "sample", "33", "ACGTN", "500000"]
+
+# docker build -t test .
+# docker run --rm -ti --name test -v "D:\Projects\fastqwiper\data:/fastqwiper/data" test paired 4 sample 33 ACGTN 500000
+# docker exec -ti test /bin/bash

.devcontainer/devcontainer.json

@@ -1,22 +1,15 @@
 // For format details, see https://aka.ms/devcontainer.json. For config options, see the
 // README at: https://github.com/devcontainers/templates/tree/main/src/docker-existing-dockerfile
 {
-	"name": "Existing Dockerfile",
-	"build": {
-		// Sets the run context to one level up instead of the .devcontainer folder.
-		"context": "..",
-		// Update the 'dockerFile' property if you aren't using the standard 'Dockerfile' filename.
-		"dockerfile": "../Dockerfile"
-	},
-	// Features to add to the dev container. More info: https://containers.dev/features.
-	"features": {
-       "ghcr.io/devcontainers/features/git:1": {}
-    },
-	"customizations" : {
-		"jetbrains" : {
-		  "backend" : "PyCharm"
-		}
-	},
-    workspaceFolder: "/fastqwiper",
-    workspaceMount: "source=${localWorkspaceFolder},target=/fastqwiper,type=bind"
+  "name": "Dockerfile FastqWiper@BFX",
+  "build": {
+    "context": "..",
+    "dockerfile": "Dockerfile"
+  },
+  // Features to add to the dev container. More info: https://containers.dev/features.
+  "features": {
+    "ghcr.io/devcontainers/features/git:1": {}
+  },
+  "workspaceFolder": "/fastqwiper",
+  "workspaceMount": "source=${localWorkspaceFolder},target=/fastqwiper,type=bind"
 }

.dockerignore

@@ -10,6 +10,4 @@ __pycache__
 
 environment.yml
 requirements.txt
-setup.py
 conda-recipe/
-logs/

.gitignore

@@ -2,6 +2,7 @@
 bbmap/
 logs/
 bbmap
+.idea/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/