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wow. communication breakdown. Part of the difficulty may be that the input is large, genomic files and the various output of each program is statistical in nature. I did not think this was of...

how would you integrate this with summary.txt in this example?
I am guessing I would put the for ... in ...
do
# All commands get piped through egrep, which then prints to stdout
...

is it possible to organize it real time? like as it is being written to file?

Here is the code for CutAdapt, where the /Processed reads/ and /Trimmed reads/ come from:
#run CutAdapt to trim...

Ah. The file stout.miRNA.bash.$date_formatted is capturing the stdout from all three programs. I am trying to extract lines from the Cutadapt stdout and the sRNAbench stdout here. The fastQC is...

I am not familiar with VAR. But the stout.miRNA.bash.$date_formatted is where /Processed reads/ and /Trimmed reads/ comes from. It was buried in my previous posting. The first few lines of the file...

Yes. I need to integrate the two output files,
summary.fastqc.$date_formatted
stout.miRNA.bash.$date_formatted
so each iteration (sample info) gets printed to file, as in my example:PASS Basic...

Ok. Here is my code #!/bin/sh -f

date_formatted=$(date +%m_%d_%y)
#outputDir=$1
speciesBuild=$1
speciesAbbrev=$2

...

ok I spent ages on my reply and then lost it when trying to post, so here it is again. bah...
You had asked

Apologies for not being totally clear. I currently have a bash script that is run...

hi,
OK. I am writing a bash script, and it is almost working for me.
Problem 1: I currently have stout sent to a file (stout.miRNA.bash.$date_formatted) which I would like to have work inside my...

thanks, I updated my input description.

Hi,
I am running my pipeline and capturing all stout from multiple programs to a .txt file. I want to go into that .txt file and search for specific lines, and finally print those lines in a second...