Friederike Hanssen

Thanks for the great input @pmoris 🙏 On a side note: making fetchngs directly output a suitable samplesheet is pretty high on our list of features we are working on...

sorry, no time yet. We'll look into it in the new year

Yes sounds great. We have a dev channel called #sarek_dev on slack as well if you need help with anything :)

looks weird indeed, can you try by providing the full path to the files as well as removing the last line? It is empty

Please open an issue with the demultiplex pipeline here: https://github.com/nf-core/demultiplex/issues

hm I can't reproduce this issue. Tested with `nextflow run main.nf -profile test,variantcalling_channels,docker --tools msisensorpro --outdir ./results` the samplesheet contains: ``` patient,sex,status,sample,cram,crai test,XX,0,sample1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai test1,XX,1,sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai test3,XX,0,sample3,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai test3,XX,1,sample4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai ``` So a mix...

I will need more info on the issue to fix.

> I think `GATK_BEDTOINTERVALLIST` should cover the BED part Probably just need to publishDir that process. Don't think we do that right now

the Hs Metric request has come up a few times. 🤞 it's in modules already and not a big thing to add :D

See also https://github.com/nf-core/sarek/issues/97