minor changes to medaka dockerfile and readme; also updated run-singu…

…larity.yml to use a different runner and more importantly apptainer github action to see if it will appropriately test singularity/apptainer functionality

.github/workflows/run-singularity.yml

@@ -20,15 +20,15 @@ on:
 jobs:
 
   build_singularity:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-24.04
     steps:
       - name: Check out Repo
         uses: actions/checkout@v4
 
       - name: Set up Singularity
-        uses: eWaterCycle/setup-singularity@v7
+        uses: eWaterCycle/setup-apptainer@v2
         with:
-          singularity-version: 3.8.3
+          apptainer-version: 1.3.5
 
-      - name: Run a singularity container
-        run: singularity run docker://${{ inputs.repository_name }}/${{ inputs.image_name }} ${{ inputs.command }}
+      - name: Run a singularity/apptainer container
+        run: apptainer run docker://${{ inputs.repository_name }}/${{ inputs.image_name }} ${{ inputs.command }}

medaka/2.0.1/Dockerfile

@@ -5,7 +5,7 @@ ARG BCFTOOLS_VER=${SAMTOOLS_VER}
 ARG HTSLIB_VER=${SAMTOOLS_VER}
 ARG MINIMAP2_VER="2.28"
 
-FROM ubuntu:jammy as builder
+FROM ubuntu:jammy AS builder
 
 ARG SAMTOOLS_VER
 ARG BCFTOOLS_VER
@@ -66,18 +66,18 @@ RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VE
     make install 
 
 RUN wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VER}/htslib-${HTSLIB_VER}.tar.bz2 && \
-    tar -vxjf htslib-${HTSLIB_VER}.tar.bz2 && \
+    tar -xjf htslib-${HTSLIB_VER}.tar.bz2 && \
     rm -v htslib-${HTSLIB_VER}.tar.bz2 && \
     cd htslib-${HTSLIB_VER} && \
     ./configure && \
     make && \
     make install 
 
 RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner && \
-    mv minimap2-${MINIMAP2_VER}_x64-linux/minimap2 /usr/local/bin
+    mv -v minimap2-${MINIMAP2_VER}_x64-linux/minimap2 /usr/local/bin
 
 ### start of app stage ###
-FROM ubuntu:jammy as app
+FROM ubuntu:jammy AS app
 
 ARG MEDAKA_VER
 ARG PYABPOA_VER
@@ -91,7 +91,7 @@ LABEL description="Consensus sequence correction provided by ONT Research"
 LABEL website="https://github.com/nanoporetech/medaka"
 LABEL license="https://github.com/nanoporetech/medaka/blob/master/LICENSE.md"
 LABEL maintainer="Curtis Kapsak"
-LABEL maintainer.email="[email protected]"
+LABEL maintainer.email="[email protected]"
 LABEL maintainer1="Erin Young"
 LABEL maintainer1.email="[email protected]"
 
@@ -132,10 +132,10 @@ ENV LC_ALL=C
 WORKDIR /data
 
 # default command is to pull up help options
-CMD medaka --help
+CMD [ "medaka", "--help" ]
 
 ### start of test stage ###
-FROM app as test
+FROM app AS test
 
 RUN apt-get update && apt-get install --no-install-recommends -y wget
 

medaka/2.0.1/README.md

@@ -1,8 +1,9 @@
-# medaka container
+# Medaka container
 
 Main tool : [medaka](https://github.com/nanoporetech/medaka)
 
 Additional tools:
+
 - bcftools version 1.21
 - samtools version 1.21
 - htslib version 1.21
@@ -16,18 +17,17 @@ Full documentation: [https://github.com/nanoporetech/medaka](https://github.com/
 ## Example Usage
 
 ```bash
-
 # listing models
 medaka tools list\_models
 
 # polishing
 medaka_consensus -i sample.fastq.gz -d sample.fasta -o medaka/sample -t 4
-
 ```
 
 ## Medaka models
 
 Medaka updates frequently. These are the medaka models in this image:
+
 ```
 Available: r103_fast_g507, r103_fast_snp_g507, r103_fast_variant_g507, r103_hac_g507, r103_hac_snp_g507, r103_hac_variant_g507, r103_sup_g507, r103_sup_snp_g507, r103_sup_variant_g507, r1041_e82_260bps_fast_g632, r1041_e82_260bps_fast_variant_g632, r1041_e82_260bps_hac_g632, r1041_e82_260bps_hac_v4.0.0, r1041_e82_260bps_hac_v4.1.0, r1041_e82_260bps_hac_variant_g632, r1041_e82_260bps_hac_variant_v4.1.0, r1041_e82_260bps_joint_apk_ulk_v5.0.0, r1041_e82_260bps_sup_g632, r1041_e82_260bps_sup_v4.0.0, r1041_e82_260bps_sup_v4.1.0, r1041_e82_260bps_sup_variant_g632, r1041_e82_260bps_sup_variant_v4.1.0, r1041_e82_400bps_bacterial_methylation, r1041_e82_400bps_fast_g615, r1041_e82_400bps_fast_g632, r1041_e82_400bps_fast_variant_g615, r1041_e82_400bps_fast_variant_g632, r1041_e82_400bps_hac_g615, r1041_e82_400bps_hac_g632, r1041_e82_400bps_hac_v4.0.0, r1041_e82_400bps_hac_v4.1.0, r1041_e82_400bps_hac_v4.2.0, r1041_e82_400bps_hac_v4.3.0, r1041_e82_400bps_hac_v5.0.0, r1041_e82_400bps_hac_variant_g615, r1041_e82_400bps_hac_variant_g632, r1041_e82_400bps_hac_variant_v4.1.0, r1041_e82_400bps_hac_variant_v4.2.0, r1041_e82_400bps_hac_variant_v4.3.0, r1041_e82_400bps_hac_variant_v5.0.0, r1041_e82_400bps_sup_g615, r1041_e82_400bps_sup_v4.0.0, r1041_e82_400bps_sup_v4.1.0, r1041_e82_400bps_sup_v4.2.0, r1041_e82_400bps_sup_v4.3.0, r1041_e82_400bps_sup_v5.0.0, r1041_e82_400bps_sup_variant_g615, r1041_e82_400bps_sup_variant_v4.1.0, r1041_e82_400bps_sup_variant_v4.2.0, r1041_e82_400bps_sup_variant_v4.3.0, r1041_e82_400bps_sup_variant_v5.0.0, r104_e81_fast_g5015, r104_e81_fast_variant_g5015, r104_e81_hac_g5015, r104_e81_hac_variant_g5015, r104_e81_sup_g5015, r104_e81_sup_g610, r104_e81_sup_variant_g610, r941_e81_fast_g514, r941_e81_fast_variant_g514, r941_e81_hac_g514, r941_e81_hac_variant_g514, r941_e81_sup_g514, r941_e81_sup_variant_g514, r941_min_fast_g507, r941_min_fast_snp_g507, r941_min_fast_variant_g507, r941_min_hac_g507, r941_min_hac_snp_g507, r941_min_hac_variant_g507, r941_min_sup_g507, r941_min_sup_snp_g507, r941_min_sup_variant_g507, r941_prom_fast_g507, r941_prom_fast_snp_g507, r941_prom_fast_variant_g507, r941_prom_hac_g507, r941_prom_hac_snp_g507, r941_prom_hac_variant_g507, r941_prom_sup_g507, r941_prom_sup_snp_g507, r941_prom_sup_variant_g507, r941_sup_plant_g610, r941_sup_plant_variant_g610
 Default consensus:  r1041_e82_400bps_sup_v5.0.0