Feature/update (#6)

* replace Docker image
* Create workflows.yml
* Update README.md
* get rid of .travis.yml

.dockstore.yml

@@ -0,0 +1,29 @@
+version: 1.2
+tools:
+  - subclass: CWL
+    primaryDescriptorPath: /bamstats.cwl
+    testParameterFiles:
+      - /test.json
+    name: bamstats_cwl
+    authors:
+      - orcid: 0000-0002-6130-1021
+  - subclass: CWL
+    primaryDescriptorPath: /bamstats_sort.cwl
+    testParameterFiles:
+      - /test.json
+    name: bamstats_sort_cwl
+    authors:
+      - orcid: 0000-0002-6130-1021
+workflows:
+  - subclass: WDL
+    primaryDescriptorPath: /bamstats.wdl
+    testParameterFiles:
+      - /test.wdl.json
+    name: wdl
+    authors:
+      - orcid: 0000-0002-6130-1021
+  - subclass: NFL
+    primaryDescriptorPath: /nextflow.config
+    name: nfl
+    authors:
+      - orcid: 0000-0002-6130-1021               

.github/workflows/workflows.yml

@@ -0,0 +1,33 @@
+name: Test workflows
+
+on: [push]
+
+jobs:
+  example_matrix:
+    strategy:
+      fail-fast: false
+      matrix:
+        lang: [cwl, wdl, nfl]
+
+    env:
+      LANGUAGE: ${{ matrix.lang }}
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Build Docker image
+      uses: docker/build-push-action@v3
+      with:
+        push: false
+        tags: quay.io/collaboratory/dockstore-tool-bamstats
+
+    - if: matrix.lang == 'cwl'
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.9'
+
+    - name: Setup engines
+      run: bash install.sh
+    - name: Run workflows
+      run: bash script.sh

README.md

@@ -1,6 +1,3 @@
-[![Docker Repository on Quay.io](https://quay.io/repository/collaboratory/dockstore-tool-bamstats/status "Docker Repository on Quay.io")](https://quay.io/repository/collaboratory/dockstore-tool-bamstats)
-[![Build Status](https://travis-ci.org/CancerCollaboratory/dockstore-tool-bamstats.svg)](https://travis-ci.org/CancerCollaboratory/dockstore-tool-bamstats)
-
 # dockstore-tool-bamstats
 
 A repo for the `Dockerfile` to create a Docker image for the BAMStats command. Also contains the
@@ -11,29 +8,20 @@ this container and describe how to call BAMStats for the community.
 
 This tool has been validated as a CWL draft-3 and v1.0 CommandLineTool. 
 
-Versions that we tested with are the following 
-```
-avro (1.8.1)
-cwl-runner (1.0)
-cwl-upgrader (0.1.1)
-cwltool (1.0.20190915164430)
-schema-salad (4.5.20190906201758)
-setuptools (25.1.6)
-```
+Versions that we tested with are documented iin https://raw.githubusercontent.com/dockstore/dockstore/1.13.0-beta.3/dockstore-webservice/src/main/resources/requirements/1.13.0/requirements3.txt
 
 
 ## Building Manually
 
-Normally you would let [Quay.io](http://quay.io) build this.  But, if you need to build
-manually you would execute:
+Normally you would let GitHub actions build this.  But, if you need to build manually (for example due to https://github.com/broadinstitute/cromwell/issues/6827)  you would execute:
 
-    docker build -t collaboratory/dockstore-tool-bamstats:1.25-7 .
+    docker build -t ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8 .
 
 ## Running Manually
 
 ```
 $ wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
-$ docker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam collaboratory/dockstore-tool-bamstats:1.25-7
+$ docker run -it -v `pwd`/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam:/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8
 
 # within the docker container
 $ /usr/local/bin/bamstats 4 /NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam
@@ -70,16 +58,16 @@ Run it using the `dockstore` CLI:
 
 ```
 # Fetch CWL workflow
-dockstore tool cwl --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 > Dockstore.cwl
+dockstore workflow cwl --entry github.com/dockstore/dockstore-tool-bamstats/bamstats_cwl:feature/update > bamstats.cwl
 
 # Make a runtime JSON template and edit it (or use the content of sample_configs.json above)
-dockstore tool convert cwl2json --cwl Dockstore.cwl > Dockstore.json
+dockstore workflow convert cwl2json --cwl bamstats.cwl > Dockstore.json
 
 # Update the "path" field for both input and output files within Dockstore.json
 jq '.bam_input.path |= "ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/NA12878/alignment/NA12878.chrom20.ILLUMINA.bwa.CEU.low_coverage.20121211.bam"| .bamstats_report.path |= "/tmp/bamstats_report.zip"' Dockstore.json | sponge  Dockstore.json
 
 # Run it locally with the Dockstore CLI
-dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats:1.25-7 --json Dockstore.json
+dockstore workflow launch --entry github.com/dockstore/dockstore-tool-bamstats/bamstats_cwl:feature/update --json Dockstore.json
 ```
 
 ### With WDL
@@ -101,11 +89,11 @@ Run it using the `dockstore` CLI:
 ```
 Usage:
 # fetch WDL
-$> dockstore tool wdl --entry quay.io/collaboratory/dockstore-tool-bamstats > Dockstore.wdl
+$> dockstore workflow wdl --entry github.com/dockstore/dockstore-tool-bamstats/wdl:feature/update > bamstats.wdl
 # make a runtime JSON template and edit it (or use the content of test.wdl.json above)
-$> dockstore tool convert wdl2json --wdl Dockstore.wdl > Dockstore.json
+$> dockstore workflow convert wdl2json --wdl bamstats.wdl > Dockstore.json
 # run it locally with the Dockstore CLI
-$> dockstore tool launch --entry quay.io/collaboratory/dockstore-tool-bamstats --json Dockstore.json
+$> dockstore workflow launch --entry github.com/dockstore/dockstore-tool-bamstats/wdl:feature/update --json Dockstore.json
 ```
 
 ## Running Nextflow Workflow

Dockstore.cwl → bamstats.cwl

@@ -15,7 +15,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-7"
+    dockerPull: "ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8"
 
 hints:
   - class: ResourceRequirement 

Dockstore.wdl → bamstats.wdl

@@ -15,7 +15,7 @@ task bamstats {
 	}
 
 	runtime {
-		docker: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-7"
+		docker: "ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8"
 		memory: mem_gb + "GB"
 	}
 

Dockstore2.cwl → bamstats_sort.cwl

@@ -15,7 +15,7 @@ dct:creator:
 
 requirements:
   - class: DockerRequirement
-    dockerPull: "quay.io/collaboratory/dockstore-tool-bamstats:1.25-7"
+    dockerPull: "ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8"
 
 inputs:
   input:

install.sh

@@ -6,11 +6,11 @@ set -o nounset
 set -o xtrace
 
 if [[ "${LANGUAGE}" == "cwl" ]]; then
-    curl -o requirements.txt "https://raw.githubusercontent.com/dockstore/dockstore/1.7.0-rc.3/dockstore-webservice/src/main/resources/requirements/1.7.0/requirements3.txt"
+    curl -o requirements.txt "https://raw.githubusercontent.com/dockstore/dockstore/1.13.0-beta.3/dockstore-webservice/src/main/resources/requirements/1.13.0/requirements3.txt"
     pip3 install --user -r requirements.txt
 elif [[ "${LANGUAGE}" == "wdl" ]]; then
     wget https://github.com/broadinstitute/cromwell/releases/download/44/cromwell-44.jar
 elif [[ "${LANGUAGE}" == "nfl" ]]; then
     curl -s https://get.nextflow.io | bash
-    mv nextflow $HOME/bin
+    cp nextflow $HOME/bin
 fi

nextflow.config

@@ -8,7 +8,7 @@ params {
 	mem_gb = '4'
 }
 
-process.container = 'quay.io/collaboratory/dockstore-tool-bamstats:1.25-7'
+process.container = 'ghcr.io/dockstore/dockstore-tool-bamstats:1.25-8'
 docker {
     enabled = true
     docker.runOptions = '-u $(id -u):$(id -g)'

script.sh

@@ -6,9 +6,9 @@ set -o nounset
 set -o xtrace
 
 if [[ "${LANGUAGE}" == "cwl" ]]; then
-    cwltool --non-strict Dockstore.cwl test.json
+    cwltool --non-strict bamstats.cwl test.json
 elif [[ "${LANGUAGE}" == "wdl" ]]; then
-    java -jar cromwell-44.jar run Dockstore.wdl --inputs test.wdl.json
+    java -jar cromwell-44.jar run bamstats.wdl --inputs test.wdl.json
 elif [[ "${LANGUAGE}" == "nfl" ]]; then
-    nextflow run main.nf
+    ./nextflow run main.nf
 fi