Error with samplesheet.csv with two column headers that have prefix in common about differentialabundance HOT 8 OPEN

I had this issue too. Probably can be fixed by changing this:

column_number=\$(cat $samples | head -n 1 | tr '$separator' "\\n" | grep -En "^$variable" | awk -F':' '{print \$1}')

to this:

column_number=\$(cat $samples | head -n 1 | tr '$separator' "\\n" | grep -En "^$variable\$" | awk -F':' '{print \$1}')

in https://github.com/nf-core/differentialabundance/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf

But the file could probably use some fixing up in general. e.g. for that line:

column_number=\$(head -n 1 $samples | tr '$separator' "\\n" | grep -En "^$variable\$" | cut -d: -f1)

I'm also unsure how many backslashes it needs.

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Alternatively, you can replace line 30 and 31 with this:

classes=\$(awk -F '$separator' 'NR==1 { for (i=1; i<=NF; i++) if (\$i == $variable) {lnum = i; next}} 1 {print \$lnum}' $samples)

One-liner with no piping.

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Which branch was this error observed on? Is there a simple test nf-cmd to trigger the error?

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To come back to the question of @asp8200, on which branch did you observe the error? I could only recreate the error on the main branch. If you pull the pipeline from the dev branch this should solve the issue.
I could not recreate the error on the dev branch.

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Looks like it's already fixed here: https://github.com/nf-core/differentialabundance/blob/dev/modules%2Fnf-core%2Fcustom%2Ftabulartogseacls%2Fmain.nf#L30

But my suggested awk-only replacement of that line and the next might still be more robust. Should I bother with a pull-request or nah?

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Hmm, I'm not familiar with the run time of awk. Could we run in some problems with the for-loop in your on-line awk option? Especially, with large datasets.

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@BEFH I will say I'm not an AWK expert, but if your code solution is more robust, do feel free to make a PR!
@jenmuell thanks for looking into this!

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