update README and Dockerfile Racon-minimap2

racon/1.5.0-minimap2/Dockerfile

@@ -59,6 +59,8 @@ LABEL base.image="ubuntu:jammy"
 LABEL dockerfile.version="1"
 LABEL software="Racon + Minimap2"
 LABEL racon.version="${RACON_VER}"
+LABEL software.version="Racon-${RACON_VER}, Minimap2-${MINIMAP2_VER}"
+LABEL racon.version="${RACON_VER}"
 LABEL minimap2.version="${MINIMAP2_VER}"
 LABEL description="Racon for assembly polishing and Minimap2 for alignment"
 LABEL website="https://github.com/lbcb-sci/racon, https://github.com/lh3/minimap2"
@@ -95,6 +97,12 @@ COPY --from=builder /racon-${RACON_VER}/test/data/* /test/
 
 WORKDIR /test
 
+# Minimap2 alignment test
+RUN wget -q https://raw.githubusercontent.com/lh3/minimap2/master/test/MT-human.fa && \
+    wget -q https://raw.githubusercontent.com/lh3/minimap2/master/test/MT-orang.fa && \
+    minimap2 -a MT-human.fa MT-orang.fa > test.sam && \
+    head test.sam
+
 # Example polishing workflow
 RUN wget -q https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf && \
   wget -q https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz && \

racon/1.5.0-minimap2/README.md

@@ -0,0 +1,46 @@
+# Racon + Minimap2 Container
+
+This container combines [Racon](https://github.com/lbcb-sci/racon) and [Minimap2](https://github.com/lh3/minimap2) for efficient polishing and alignment in long-read assembly workflows.
+
+## Tools Included
+- **Racon**: Polishes long-read assemblies.
+- **Minimap2**: Generates alignments for use with Racon and other polishing tools.
+
+### Code Repositories
+- Racon: [GitHub Repository](https://github.com/lbcb-sci/racon)
+- Minimap2: [GitHub Repository](https://github.com/lh3/minimap2)
+
+## Basic Information
+
+### Racon
+- **Executable**: `racon`
+- **Help**: `racon -h`
+- **Version**: `racon -v`
+- **Description**: 
+  > Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods that do not include a consensus step.
+
+### Minimap2
+- **Executable**: `minimap2`
+- **Help**: `minimap2 -h`
+- **Version**: `minimap2 --version`
+- **Description**: 
+  > Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
+
+## Example Usage
+
+```bash
+# Racon general
+racon <sequences> <overlaps> <target sequences>
+
+# more specific
+racon --match 8 --mismatch -6 --gap -8 --window-length 500 --threads {threads} {input.reads} {input.alignment} {input.assembly}
+
+#Combined Racon and Minimap2 Workflow
+
+#Align Reads to Assembly Using Minimap2:
+minimap2 -x map-ont <assembly.fasta> <reads.fastq> > overlaps.paf
+
+#polish assembly using Racon
+racon --threads {threads} <reads.fastq> overlaps.paf <assembly.fasta> > polished_assembly.fasta
+```
+

racon/1.5.0/README.md

@@ -1,46 +1,23 @@
-# Racon + Minimap2 Container
+# racon container
 
-This container combines [Racon](https://github.com/lbcb-sci/racon) and [Minimap2](https://github.com/lh3/minimap2) for efficient polishing and alignment in long-read assembly workflows.
+Main tool : [racon](https://github.com/lbcb-sci/racon)
 
-## Tools Included
-- **Racon**: Polishes long-read assemblies.
-- **Minimap2**: Generates alignments for use with Racon and other polishing tools.
+Code repository: https://github.com/lbcb-sci/racon
 
-### Code Repositories
-- Racon: [GitHub Repository](https://github.com/lbcb-sci/racon)
-- Minimap2: [GitHub Repository](https://github.com/lh3/minimap2)
+Basic information on how to use this tool:
+- executable: racon
+- help: -h
+- version: -v
+- description: Polishes long read assemblies
 
-## Basic Information
+> Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step.
 
-### Racon
-- **Executable**: `racon`
-- **Help**: `racon -h`
-- **Version**: `racon -v`
-- **Description**: 
-  > Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods that do not include a consensus step.
-
-### Minimap2
-- **Executable**: `minimap2`
-- **Help**: `minimap2 -h`
-- **Version**: `minimap2 --version`
-- **Description**: 
-  > Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database.
-
-## Example Usage
+# Example Usage
 
 ```bash
-# Racon general
+# general
 racon <sequences> <overlaps> <target sequences>
 
 # more specific
 racon --match 8 --mismatch -6 --gap -8 --window-length 500 --threads {threads} {input.reads} {input.alignment} {input.assembly}
-
-#Combined Racon and Minimap2 Workflow
-
-#Align Reads to Assembly Using Minimap2:
-minimap2 -x map-ont <assembly.fasta> <reads.fastq> > overlaps.paf
-
-#polish assembly using Racon
-racon --threads {threads} <reads.fastq> overlaps.paf <assembly.fasta> > polished_assembly.fasta
-```
-
+```