Stephen Kelly

4451 add vcf2maf nf test

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## PR checklist Closes [#4451](https://github.com/nf-core/modules/issues/4451) - [x] This comment contains a description of changes (with reason). - [x] If you've fixed a bug or added code that should be tested,...

BLAST Database error: No alias or index file found for nucleotide database [ncbi-blast-db/db] in search path

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I was trying to run this pipeline as described, using the Docker container, but get this error: ``` $ ./nextflow run cbcrg/piper-nf -with-docker N E X T F L O...

Need the ability to skip md5 check for some files in snapshot

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I am trying to avoid taking the md5sum for some files in my snapshot. I found this example of one potential method that was shared online [here](https://github.com/nf-cmgg/germline/blob/5ad1ca9213d4017a99cd94d6ffb54a12f6274105/tests/pipeline/gvcfs/main.nf.test#L27), which I have...

Ability to use custom email template string instead of file

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The current implementation of custom email templates uses a separate [template file](https://github.com/nextflow-io/nextflow/blob/master/modules/nextflow/src/main/resources/nextflow/mail/notification.txt), like this; https://www.nextflow.io/docs/latest/config.html#scope-notification ```groovy notification { enabled = true template = "assets/mail/notification.txt" } ``` Can we have this...

Added extra dev build and run instructions. Also merged the two `nextflow.config` files, and added a `tag` to the `test.nf` and an extra process using `exec` to the workflow to...

Nextflow processes with `exec` do not show up in the Legacy Renderer

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Just an observation, not sure if this is intentional or a known issue, but if you have a Nextflow process like this ```groovy process EXEC_FOO { input: tuple val(prefix), val(constant)...

"cleanup" option does not remove staged files from S3

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## Bug report When using Nextflow with the `cleanup = true` option, input files staged from S3 are left in the work dir. ### Expected behavior and actual behavior In...

the Nextflow DAG should render as a subway plot

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There have been many Issues and support tickets related to new and better ways to render the pipeline DAG especially for use with presentations and repo README's I think the...