CODEWITHSUNDEEP
gnu-parallel
Arun
Arun

Reputation: 669

Error in GNU parallel dynamic string replacement

I have more than 50 file pairs with names in the following format: AA-7R-76L1.clean.R1.fastq.gz, AA-7R-76L1.clean.R2.fastq.gz

I tried to use parallel in the following way:

parallel --plus echo {%R..fastq.gz} ::: *.fastq.gz |parallel 'repair.sh in1={}.R1.fastq.gz in2={}.R2.fastq.gz out1={}.repd.R1.fastq.gz out2={}.repd.R2.fastq.gz outs={}.singletons.fastq.gz repair'

--plus echo should dynamically replace R1.fastq.gz, R2.fastq.gz to capture the sample name i.e.HB-7R-25L0.clean. It should then feed it to repair.sh

The error I get is, the first section extracts the entire filename and does not capture the sample name. Thus in1 and in2 becomes AA-7R-76L1.clean.R1.fastq.gz.R1.fastq.gz and AA-7R-76L1.clean.R2.fastq.gz.R2.fastq.gz

What is the error here?

Upvotes: 2

Views: 68

Answers (1)

Ole Tange
Ole Tange

Reputation: 33685

Something like:

$ parallel --plus --dry-run  'repair.sh in1={} in2={/R1/R2} out1={/R1/fixed.R1} out2={/R1/fixed.R2} outs={%.R1.fastq.gz}_singletons.fastq repair' ::: *R1.fastq.gz

(Assuming R1 and R2 is not part of the *-part of the name).

Upvotes: 1

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