Filter called variants by user specified bed file #627
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dennishendriksen
requested changes
Jul 15, 2024
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for the 'Nanopore in de Diagnostiek' project we start from fastq and cannot use --bed. I think it should be added to the fastq workflow as well and thus should be a common sample sheet property.
how about renaming --bed to --regions to allow for future support of .tsv or plaintext input?
dennishendriksen
requested changes
Jul 17, 2024
bartcharbon
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dennishendriksen
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Jul 18, 2024
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fastq/nanopore_adaptive_sampling | PASSED | 253024=completed output/fastq/nanopore_adaptive_sampling/.nxf.log
fastq/nanopore | PASSED | 253025=completed output/fastq/nanopore/.nxf.log
fastq/pacbio_hifi | PASSED | 253026=completed output/fastq/pacbio_hifi/.nxf.log
cram/complex | PASSED | 249737=completed output/cram/complex/.nxf.log
cram/multiproject | PASSED | 249738=completed output/cram/multiproject/.nxf.log
cram/nanopore_duo | PASSED | 249739=completed output/cram/nanopore_duo/.nxf.log
cram/nanopore | PASSED | 249740=completed output/cram/nanopore/.nxf.log
cram/single | PASSED | 249741=completed output/cram/single/.nxf.log
cram/trio | PASSED | 249742=completed output/cram/trio/.nxf.log
vcf/aip | PASSED | 250015=completed output/vcf/aip/.nxf.log
vcf/chd7 | PASSED | 250016=completed output/vcf/chd7/.nxf.log
vcf/corner_cases | PASSED | 250017=completed output/vcf/corner_cases/.nxf.log
vcf/deb_register | PASSED | 250018=completed output/vcf/deb_register/.nxf.log
vcf/empty_input | PASSED | 250019=completed output/vcf/empty_input/.nxf.log
vcf/empty_output_filter_samples | PASSED | 250020=completed output/vcf/empty_output_filter_samples/.nxf.log
vcf/empty_output_filter | PASSED | 250021=completed output/vcf/empty_output_filter/.nxf.log
vcf/filter_samples | PASSED | 250022=completed output/vcf/filter_samples/.nxf.log
vcf/liftover | PASSED | 250023=completed output/vcf/liftover/.nxf.log
vcf/multiproject_classify | PASSED | 250024=completed output/vcf/multiproject_classify/.nxf.log
vcf/mvid | PASSED | 250025=completed output/vcf/mvid/.nxf.log
vcf/str | PASSED | 250026=completed output/vcf/str/.nxf.log
vcf/trio | PASSED | 250027=completed output/vcf/trio/.nxf.log
vcf/vkgl_lb | PASSED | 250028=completed output/vcf/vkgl_lb/.nxf.log
vcf/vkgl_lp | PASSED | 250029=completed output/vcf/vkgl_lp/.nxf.log
vcf/vkgl_vus | PASSED | 250030=completed output/vcf/vkgl_vus/.nxf.log
End-to-end tests are not executed by Travis CI, please execute manually:
APPTAINER_BIND=$PWD bash test/test.shpasses