Harshil Patel comments

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                                            Harshil Patel

Add new testing strategy based on nf-test files

This snippet should fix the linting with the `actions_ci` https://github.com/nf-core/fetchngs/blob/8ec2d934f9301c818d961b1e4fdf7fc79610bdc5/.nf-core.yml#L2-L3

Having issues similar to #1003 "FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_INDEX is launched multiple times and fails"

Hi @Jgarlan1 ! Unfortunately, I can't read the image you have uploaded in your initial comment to make any sense of what the issue might be here. Are you able...

Add example of dynamic directive with input file

There are some other real-world examples in this talk: https://youtu.be/oAdSpdUrJag?t=16928 Would be awesome to have something like this to tune resources.

Adding WGCNA to the workflow?

As mentioned, in my previous comment this will be out of the scope of this pipeline. Thanks for the suggestion!

add optional argument to let infer_experiment.py decide strandedness

Implemented in https://github.com/nf-core/rnaseq/pull/910 If you set the strandedness value to `auto` in the input samplesheet, the pipeline will sub-sample the input FastQ files to 1 million reads, use Salmon Quant...

Custom error messages for file schema validation

Closing this as we now have the nf-validation plugin which takes care of all of this and more!

all `salmon.merged.gene_tpm*.tsv` files contain the same exact values

Hi @rob-p ! Would love your input on this please?

Unclear description of output files for alignment and quantification step

@danwiththeplan @danielsu0523 @schaffman5 were the changes @ctuni added in https://github.com/nf-core/rnaseq/pull/885 satisfactory to clarify the points you raised here? If not, be great if you are able to suggest what else...

Unclear description of output files for alignment and quantification step

Closing for now but feel to re-open this or a new issue (or a PR!) if required.

SALMON_TX2GENE failing when skip_alignment is true and pseudo_aligner is salmon

Thanks @ejseqera ! Given that this has been tested in the latest release I will close this issue. Please feel free to reopen if the issue persists.