Questions tagged [nextflow]
The nextflow tag has no usage guidance.
5
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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 ...
- 255
2
votes
1
answer
2k
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Merge multiple channels each emits multiple files in nextflow
I need to merge multiple channels each emits multiple file. So far I did something as below:
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- 307
1
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1
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105
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Nextflow - Missing value declared as output parameter - output variable defined in script
I've normal-tumor human FASTQ file(s). Currently, I work with only one sample (both normal and tumor fastq R1 and R2), only.
I have alignment gatk mark duplicates, setupnmdtags, applybqsr, recalibrate ...
- 255
1
vote
1
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1k
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Nextflow: ordering the execution of processes; outputs of process A are inputs of process B
I need to build a pipeline where 2nd process starts after completion of the 1st process and the 3rd after 2nd. As I understand nextflow's processes run parallel. But I need it to run in a order 1st>...
- 307
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580
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parse csv/text file to create a channel with array in nextflow
[![example csv file][1]][1]
First I want to start by parsing and doing some operation on a text/csv file. How could I read a csv/text file in nextflow?
Suppose, I have above csv file with 3 columns. ...
- 307