Documentation for applying sarek to nf-core test data

[bnwlf]

Hi, I have some serious problems to apply sarek to the nf-core test data. I am searching for the specific nextflow call that generates the sarek outputs of the test for the nf-core test data. I could not find any explicit command in the readme.

Thanks! Ben

[maxulysse]

Hi @bnwlf.

Test data (and corresponding references) in https://github.com/nf-core/test-datasets is in the sarek branch. Using the test profile will use the specific test config file: https://github.com/nf-core/sarek/blob/master/conf/test.config Input file is mainly this tsv file: https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/tsv/tiny-manta-https.tsv that contain https path to the different fastq pairs. In this repository there is all the other tsv files than can be used for testing. If the file end with -https.txt path to fastq/bam is with https otherwise, it's assuming you used git clone to download the test-datasets repo in the data folder within the current directory.

Several tests are actually run with GitHub Actions (cf https://github.com/nf-core/sarek/blob/master/.github/workflows/ci.yml). But the Nextflow command that I generally use to test is nextflow run nf-core/sarek -profile test,docker (it tests preprocessing, which is I think the critical part). To have a more complete experience, you can add --tools Strelka,Manta,HaplotypeCaller

I hope I replied to your questions. Don't hesitate if you have need more clarification.

[maxulysse]

It will be good also to add information about that in the nf-core/sarek repo in the troubleshooting section of the usage documentation