fixed typos

StaPH-B · Sep 6, 2023 · 0e0e0d3 · 0e0e0d3
1 parent c835111
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diff --git a/artic/1.2.4-1.9.1/Dockerfile b/artic/1.2.4-1.9.1/Dockerfile
@@ -93,12 +93,12 @@ WORKDIR /test
 
 # using on "real" data (sample files were not sequenced with version 5.3.2 primers)
 RUN wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR224/050/SRR22452250/SRR22452250_1.fastq.gz && \
-    artic guppyplex --min-length 400 --max-length 700  --directory . --prefix SRR22452250_1.fastq.gz --output SRR22452250_1_filtered.fastq.gz && \
-    mkdir -p dir/name/v5 && \
-    wget https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed      -O dir/name/v5/name.primer.bed && \
-    wget https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta -O dir/name/v5/name.reference.fasta && \
-    wget https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.scheme.bed      -O dir/name/v5/name.scheme.bed && \
-    samtools faidx dir/name/v5/name.scheme.bed && \
-    artic minion --normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360 --threads 4 --read-file SRR22452250_1_filtered.fastq.gz --scheme-directory dir --scheme-version 5 name final && \
+    artic guppyplex --min-length 400 --max-length 700  --directory . --prefix SRR22452250_1.fastq.gz --output SRR22452250_1_filtered.fastq.gz && \ 
+    mkdir -p dir/name/V5 && \
+    wget -q https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.primer.bed      -O dir/name/V5/name.primer.bed && \
+    wget -q https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.reference.fasta -O dir/name/V5/name.reference.fasta  && \
+    wget -q https://raw.githubusercontent.com/artic-network/primer-schemes/master/nCoV-2019/V5.3.2/SARS-CoV-2.scheme.bed      -O dir/name/V5/name.scheme.bed && \
+    samtools faidx dir/name/V5/name.reference.fasta && \
+    artic minion --normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360 --threads 4 --read-file SRR22452250_1_filtered.fastq.gz --scheme-directory ./dir --scheme-version 5 name final && \
     ls final*
 
diff --git a/artic/1.2.4-1.9.1/README.md b/artic/1.2.4-1.9.1/README.md
@@ -3,6 +3,7 @@
 Main tool : [artic](https://github.com/artic-network/fieldbioinformatics)
 
 Additional tools:
+
 - medaka=1.9.1
 
 Full documentation: [https://github.com/artic-network/fieldbioinformatics](https://github.com/artic-network/fieldbioinformatics)
@@ -12,7 +13,7 @@ And additional documentation: [https://artic.readthedocs.io/en/latest/](https://
 
 > A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore.
 
-WARNING : This container does not contain nanopolish, nor does it contain the primer schemes found at https://github.com/artic-network/primer-schemes. Those will have to be downloaded and mounted separately.
+WARNING : This container does not contain the primer schemes found at [https://github.com/artic-network/primer-schemes](https://github.com/artic-network/primer-schemes). Those will have to be downloaded and mounted separately.
 
 ## Example Usage with the artic primers
 
@@ -32,7 +33,9 @@ docker run -v $(pwd):/data staphb/artic:latest artic minion --normalise 200 --sk
 # the result files will all start with test*
 ```
 
-In general, any primer scheme can be used as long as it meeds artic's requirments. This is the recommended directory structure with corresponding files:
+In general, any primer scheme can be used as long as it meeds [artic's requirments](https://github.com/artic-network/primer-schemes).
+
+This is the recommended directory structure with corresponding files:
 
 ```bash
 ${diretory}/${name}/V${version}/${name}.primer.bed
@@ -41,7 +44,14 @@ ${diretory}/${name}/V${version}/${name}.reference.fasta
 ${diretory}/${name}/V${version}/${name}.reference.fasta.fai
 ```
 
-The command to use this primer scheme would be 
+The command to use this primer scheme would be
+
 ```bash
 artic minion --normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360 --threads 4 --read-file input.fastq.gz --scheme-directory ${directory} --scheme-version ${version} ${name} outputprefix
-```
+```
+
+Different primer schemes can be validated via artic-tools (already in PATH) via
+
+```bash
+artic-tools validate_scheme ${basename}.primer.bed --outputInserts ${basename}.insert.bed
+```