in bio-cwl-tools/subread/featureCounts.cwl

I didn't see RSEM available as a tool here. Is RSEM available?

Issue to acknowledge contributors using https://allcontributors.org/docs/en/bot/usage

https://www.commonwl.org/v1.0/CommandLineTool.html#SoftwareRequirement

It looks like fastq_dump.cwl might have some problems when running without Internet connection. fastq-dump downloads something even when extracting data from the previously downloaded sra file.

Essential:

• Author
• Description

Others:

• Topic (keywords?)
• License of wrapped tool (#4)

See https://github.com/Barski-lab/workflows/blob/master/tools/bamtools-stats.cwl for ideas

What should go into a PR template for this repository? I'd like to propose the following:

• Radio button with options:
  This PR adds a new tool descriptor
  This PR updates a tool descriptor
  This PR does something else
• Check box: "I have read the CONTRIBUTING.md" document
• Check box: "I am making this work available under the terms of the Apache License 2.0 (as per the LICENSE file)"

And then as a stop-gap for testing, perhaps we can ask that the test in the tests/ folder be run by the contributor and the cwltool output of running the test is appended as a comment in the PR. I'm not sure exactly how to work this but more importantly, what do others think about this? It will at least ensure that contributed tools are working.

Then on the last check box proposed above, how does that relate to the public domain donations issue? And do / should tool contributors retain copyright to their tools?

Finally, what else is there to add to such a template?

Sir,

I have to write CWL script for variant calling using VARSCAN and samtools separately. I do not find VARSCAN as well as samtools_mpileup into the cwl tool repository.

How to form CWL script using them?

Hi, I've tested the Kallisto-Quant.cwl with

InputReads:
    - class: File
      path: ../../rnaseq/sample1-1.fastq.gz
    - class: File
      path: ../../rnaseq/sample1-2.fastq.gz
Index:
  class: File
  path: ../../kallisto-index-biocwl/output/Fbid
isSingle: true  
FragmentLength: 200
StandardDeviation: 20  
BootstrapSamples: 0
PseudoBam: false

Unfortunately the output is not wired properly.

("Error collecting output for parameter 'quantification_h5': Kallisto-Quant.cwl:129:7: Did not find output file with glob pattern: ['out/abundances.h5'].", {})

I am new to CWL, so not sure how to fix and PR.

[DEPRECATION NOTICE] Docker Image Format v1 and Docker Image manifest version 2, schema 1 support is disabled by default and will be removed in an upcoming release. Suggest the author of quay.io/biocontainers/subread:1.5.0p3--0 to upgrade the image to the OCI Format or Docker Image manifest v2, schema 2. More information at https://docs.docker.com/go/deprecated-image-specs/

• quay.io/biocontainers/bowtie2:2.3.0--py36_1
• quay.io/biocontainers/bwa:0.7.17--ha92aebf_3
• quay.io/biocontainers/crossmap:0.2.7--py27_0
• quay.io/biocontainers/fastp:0.20.0--hdbcaa40_0
• quay.io/biocontainers/gatk4:4.1.1.0--0
• quay.io/biocontainers/gatk4:4.1.3.0--0
• quay.io/biocontainers/kallisto:0.45.0--hdcc98e5_0
• quay.io/biocontainers/kraken2:2.0.8_beta--pl526h6bb024c_0
• quay.io/biocontainers/mashmap:2.0--gsl2.2_1
• quay.io/biocontainers/minimap2:2.17--h8b12597_1
• quay.io/biocontainers/multiqc:1.7--py_4
• quay.io/biocontainers/phantompeakqualtools:1.2--1
• quay.io/biocontainers/pizzly:0.37.3--0
• quay.io/biocontainers/seqkit:0.7.1--0
• quay.io/biocontainers/snp-sites:2.5.1--hed695b0_0
• quay.io/biocontainers/spades:3.13.0--0

https://www.commonwl.org/v1.2/CommandLineTool.html#CommandLineTool (scroll to intent)

An identifier for the type of computational operation, of this Process. Especially useful for "class: Operation", but can also be used for CommandLineTool, Workflow, or ExpressionTool.

If provided, then this must be an IRI of a concept node that represents the type of operation, preferably defined within an ontology.

For example, in the domain of bioinformatics, one can use an IRI from the EDAM Ontology's Operation concept nodes, like Alignment, or Clustering; or a more specific Operation concept like Split read mapping.

Will be useful to the Workflomics project, amongst others.

I think this is probably a mistake, but anyway, this tool doesn't seem to work as this container doesn't actually contain the STAR executable.

https://github.com/galaxyproject/tpv-shared-database/blob/main/tools.yml

Do a single sweep of existing tools, and add to the checklist for new contributions

Currently the CI runs on all cwl files, if we plan to integrate execution tests then we need to identify the proper mechanism of doing this via pull requests.

https://github.com/truwl/biocondastats/blob/main/top100.tsv

Generated from Jeremy's tool.

$ python ci.py

fatal: ambiguous argument 'release..FETCH_HEAD': unknown revision or path not in the working tree.

Use '--' to separate paths from revisions, like this:

'git <command> [<revision>...] -- [<file>...]'

Traceback (most recent call last):

  File "ci.py", line 9, in <module>

    changed_files = check_output("git --no-pager diff --name-status release..FETCH_HEAD", shell=True)

  File "/opt/python/3.7.1/lib/python3.7/subprocess.py", line 389, in check_output

    **kwargs).stdout

  File "/opt/python/3.7.1/lib/python3.7/subprocess.py", line 481, in run

    output=stdout, stderr=stderr)

subprocess.CalledProcessError: Command 'git --no-pager diff --name-status release..FETCH_HEAD' returned non-zero exit status 128.

https://travis-ci.com/common-workflow-library/bio-cwl-tools/jobs/248764797

Create a script that can be used (via a github action?) to automatically generate a complete .dockstore.yml that contains entries for all tools in the repo. This would be a follow-on to #139, which added a .dockstore.yml file for the existing tools, and instructions in CONTRIBUTING.md about how to update it for a new tool.

Here we need to decide the structure of the this repository. As it was agreed, every tool should be placed in a separate directory. The questions are:

• should we keep Dockerfile in the same folder?
• where do we put job files for testing?
• where do we keep input data for testing jobs?

Only 3 entries there have associated CWL tool descriptions: https://bio.tools/api/t/?downloadType=CWL

Possibly by doing a bulk-update to https://github.com/research-software-ecosystem/content

At the moment I have a number of PRs open against this repository, and I have opened a discussion on moving this repository forward. I would like to see a few things addressed:

1. Adding a PR template
2. Increasing the pool of people who are contributors to the repository
3. Developing the expectations for tool testing and testing infrastructure further
4. Developing best practice for using bio-cwl-tools in your own workflows (also see this) discussion

Please comment below if you think this is a reasonable programme of action and if you would like to contribute.

Do we require the Dockerfile be present here as well?