Questions tagged [looper]

A job submitter that uses Portable Encapsulated Projects

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1answer
28 views

Adding new columns to this data frame

I have a dataframe like this ...
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2answers
100 views

How I can run this code on my files?

I am annotating some .txt files by Annovar software by this code nnovar]$ module load annovar/2016Feb01 [cyan01 annovar]$ table_annovar.pl But I really got ...
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1answer
79 views

How I move these files based on their names in R or terminal

EDITED I have list of my samples in first column and corresponding file name for my .vcf files in second column of a file name clin_name.txt like below. For ...
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1answer
37 views

Replacing some strings in R or terminal

I have a .txt file; I have 139 unique sample IDs in sampleID column ...
0
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1answer
44 views

Looper: can't specify the individual path for one pipeline run

I have multiple samples that I need to run one pipeline on. I am using Looper: https://github.com/pepkit/looper I have a real trouble specifying a separate location for each pipeline output files. ...
1
vote
1answer
37 views

Looper: missing argument error

While trying to run looper I am getting the following error: Error (missing attribute): 'sandro_rna_seq' requires sample attribute '/scratch/nv4e/sandro_looper/pipeline/jyvo_experiment-metadata....
1
vote
1answer
20 views

Looper: Duplicate sample name error

I am using Looper. While running looper run project_config.yaml I am getting duplicate sample name error. I have two ...