needlestack
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IARCbioinfo
Multi-sample somatic variant caller
When running the example data test, got an error message saying that "Nextflow DSL1 is no longer supported — Update your script to DSL2, or use Nextflow 22.10.x or earlier"....
Hi, i am trying to run the program using: ``` nextflow run iarcbioinfo/needlestack -with-docker --bed bed/SOPHIA_targetregions_hg19.bed --input_bams bam/SOPHIA/ --ref ref/ucsc.hg19.fasta --output_vcf output/SOPHIA_needlestack.vcf ``` The bed file is sorted, the bam...
Hi there, Do you have any advice about running needlestack on a large number of samples on google cloud? Any chance you have a config already for it? Do all...
We should adapt our CircleCI tests to the new 2.0 version. Follow the [guidelines](https://circleci.com/sunset1-0/?mkt_tok=eyJpIjoiT0RZd09HSmpaV1ZqWXpZeSIsInQiOiJ0VGFIeEJKeEFrQU40aEdEWFwvM1NZd0dISkltS2htZ0lUdkU2XC93WGNXb0NnTk5xQmU4Z09uR2FadFBiVzIwYzZzaHoyTkkremFnTzRCMzdjRVpIWnJEclEyVXQwM3pcL2JnS3RZYWZFN3p5Zm55RVFFT1pHdTkxWVd4TndYbmc5QyJ9), and take example of their [webinars](https://www.youtube.com/watch?v=xOSHKNUIkjY). With 2.0, the CircleCi yaml file would not be `circle.yml`...
Adding the `--no-BAQ` in `samtools mpileup` causes: > Disable probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned....
https://icors2016.sciencesconf.org/conference/icors2016/Yohai.pdf http://www.matematica.uns.edu.ar/uma2016/material/comunicaciones/estadistica/Valdora.pdf https://www.birs.ca/workshops/2015/15w5003/files/Alfio_Marazzi_Banff.pdf
Add more description on the executed command, e.g. output also: * --map_qual and --base_qual thresholds * working directory path
Could you please find alternate name shortenings for allelic fraction and allele frequency instead of AF for both? Thanks :)
Currently the `--output_vcf` parameter can only be the name of the file and not the full path (see https://github.com/IARCbioinfo/needlestack/blob/v1.1b/needlestack.nf#L505 and https://groups.google.com/forum/#!topic/nextflow/ctLboXGPdwI), and the path can be given using `--output_folder`. The...
The bed process does not have any input specified but still accesses to file specified by the params. This I think is dangerous, normally files used in the script are...
