Comments (8)
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}')
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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Related Issues (20)
- URGENT: pin nf-validation version HOT 2
- Dev version: On parameters website list parameter gene_sets_files in section GSEA HOT 1
- Name of blocking variable not correctly recognized HOT 7
- Continuous covariates HOT 8
- Please pin the version of the nf-validation plugin! HOT 1
- release differentialabundance HOT 1
- Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode)` terminated with an error exit status (125) HOT 4
- Error in TABULAR_TO_GSEA_CHIP HOT 1
- GSEA html reports have broken links to png and TSV files HOT 1
- Failed to publish file => double forward slashes
- Auto-format sample names HOT 2
- PosixFileAttributeView
- Missing colour and hover labels in interactive report volcano plot HOT 4
- Normalized/Raw data mishap on the report HOT 1
- Provide a parameter to disable rmarkdown report creation in the differential abundance pipeline HOT 2
- Requests: Enhancements to DESeq2 csv outputs and PDF outputs
- For spike-in analysis, remove control features from outputs
- How to use `--transcript_length_matrix` with nf-core/rnaseq `--aligner star_rsem` output? HOT 2
- volcano plot cannot be edited in the report HOT 3
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