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Results tagged with nextflow
Search options questions only
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user 862
2
votes
1
answer
128
views
nextflow: merge lane files from samples forward and reverse read
I'd like to merge files from different lanes for forward and reverse reads. For e.g., if a sample A has three lanes in forward, and three reverse, ultimately one reverse and one forward is to be gener …
- 2,498
1
vote
1
answer
128
views
nextflow: unable to find index
I've a pipeline with many processes.
One of the steps is to run lancet tool. Lancet tool runs per chromosome (1-22, x,y). The input in the lancet step is output from the applybqsr (gatk).
There are tu …
- 1,511
1
vote
1
answer
213
views
Nextflow - Missing value declared as output parameter - output variable defined in script
fastq.gz
tiny_tumor_R2.fastq.gz
tiny_normal_R1.fastq.gz
tiny_normal_R2.fastq.gz
The expected output from the mutect2 is tiny.mutect2out.vcf that is ${sample_name}".mutect2out.vcf"
I split tiny_normal using nextflow …
- 3,287
4
votes
1
answer
160
views
nextflow: tumor normal sample - how to make code organic
I'm developing pipeline in nextflow it uses tools: fastp, bwa mem index, bwamem, gatk mark duplicates, gatk setupnmd, gatk applybqsr, gatk recalibrate. …
- 3,287
2
votes
0
answers
134
views
Nextflow: pass reads variable to process in another script
This question has been asked and answered on Stack Overflow
I'm new to nextflow, channel, process. Kindly bear with me. I'd like to create a pipeline, pass paired reads from one to another process. …
- 15.1k