blobltoolkit i/o subworkflow

[alxndrdiaz]

PR checklist

• [ ] This comment contains a description of changes (with reason).
• [ ] If you've fixed a bug or added code that should be tested, add tests!
  • [ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • [ ] If necessary, also make a PR on the nf-core/blobtoolkit branch on the nf-core/test-datasets repository.
• [ ] Make sure your code lints (nf-core lint).
• [ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• [ ] Usage Documentation in docs/usage.md is updated.
• [ ] Output Documentation in docs/output.md is updated.
• [ ] CHANGELOG.md is updated.
• [ ] README.md is updated (including new tool citations and authors/contributors).

Issue: i/o automate input subworkflow #26

This PR is part of the Google Summer of Code 2022 project: Conversion of the BlobToolKit pipeline to Nextflow, GitHub repository: https://github.com/sanger-tol/blobtoolkit

[alxndrdiaz]

For the 2 failing checks :

Run nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results
N E X T F L O W  ~  version 21.10.3
Launching `/home/runner/work/blobtoolkit/blobtoolkit/main.nf` [angry_leakey] - revision: ebef3e10d4
Cannot enable more than one container engine -- Choose either one of: docker, singularity

Uses Docker while conf/test.config (lines 24 to 27) is using Singularity:

// Singularity settings - normally provided through `conf/sanger.config`
singularity.enabled    = true
singularity.autoMounts = true
singularity.runOptions = '--bind /lustre --bind /nfs'

[priyanka-surana]

Did your tests run successfully in the farm?

[alxndrdiaz]

Did your tests run successfully in the farm?

No:

nextflow run main.nf -profile test,singularity

Gives the following Nextflow error:

ERROR: Validation of pipeline parameters failed!
* Missing required parameter: --input

[muffato]

@alxndrdiaz: the last two commits (d3542727a06b2e40438846abf9bd499fd7692a89 and 4721f526212b06fc1be6897026dae7b2fa7d8a24) shouldn't be there. They're undoing some recent changes we've pushed to the automate_io (adding proper versioning in all Python and Shell scripts)

[alxndrdiaz]

@alxndrdiaz: the last two commits (d354272 and 4721f52) shouldn't be there. They're undoing some recent changes we've pushed to the automate_io (adding proper versioning in all Python and Shell scripts)

I just merged those changes, but if there is anything that has to be modified just let me know.

[alxndrdiaz]

Using:

nextflow run main.nf -profile test,singularity

Gives the following output:

executor >  local (6)
[80/eef32d] process > NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:INPUT_TOL (1)                       [100%] 1 of 1 ✔
[69/5684d5] process > NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:INPUT_CHECK:SAMPLESHEET_CHECK (samplesheet.csv) [100%] 1 of 1 ✔
[1c/a00e46] process > NFCORE_BLOBTOOLKIT:BLOBTOOLKIT:SAMTOOLS_VIEW (mMelMel3_T2)                     [100%] 4 of 4 ✔

-[nf-core/blobtoolkit] Pipeline completed successfully-
WARN: There's no process matching config selector: CUSTOM_DUMPSOFTWAREVERSIONS
WARN: There's no process matching config selector: FASTQC
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: blobtoolkit/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location