Rnaseq: Docker test failure

[mjsteinbaugh]

I'm seeing this error pop up for the Docker test:

conda activate [email protected]
nextflow run nf-core/rnaseq -profile test,docker

[96/fe8030] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_GENE (salmon_tx2gene.tsv)                             [100%] 1 of 1 ✔
[57/5c3134] process > RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv)                       [100%] 1 of 1, failed: 1 ✘
[31/ea5755] process > RNASEQ:DESEQ2_QC_SALMON                                                                [100%] 1 of 1 ✔
[-        ] process > RNASEQ:GET_SOFTWARE_VERSIONS                                                           -
[-        ] process > RNASEQ:MULTIQC                                                                         -
Execution cancelled -- Finishing pending tasks before exit
Error executing process > 'RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv)'

Caused by:
  Process `RNASEQ:QUANTIFY_SALMON:SALMON_SE_TRANSCRIPT (salmon_tx2gene.tsv)` terminated with an error exit status (1)

Command executed:

  salmon_summarizedexperiment.r NULL salmon.merged.transcript_counts.tsv salmon.merged.transcript_tpm.tsv
  Rscript -e "library(SummarizedExperiment); write(x=as.character(packageVersion('SummarizedExperiment')), file='bioconductor-summarizedexperiment.version.txt')"

Command exit status:
  1

Command output:
  (empty)

Command error:
  The following objects are masked from 'package:base':

      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which, which.max, which.min

  Loading required package: S4Vectors

  Attaching package: 'S4Vectors'

  The following object is masked from 'package:base':

      expand.grid

  Loading required package: IRanges
  Loading required package: GenomeInfoDb
  Loading required package: Biobase
  Welcome to Bioconductor

      Vignettes contain introductory material; view with
      'browseVignettes()'. To cite Bioconductor, see
      'citation("Biobase")', and for packages 'citation("pkgname")'.

  Loading required package: DelayedArray
  Loading required package: matrixStats

  Attaching package: 'matrixStats'

  The following objects are masked from 'package:Biobase':

      anyMissing, rowMedians


  Attaching package: 'DelayedArray'

  The following objects are masked from 'package:matrixStats':

      colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

  The following objects are masked from 'package:base':

      aperm, apply, rowsum

  Error in rbind(deparse.level, ...) :
    numbers of columns of arguments do not match
  Calls: rbind ... standardGeneric -> eval -> eval -> eval -> rbind -> rbind
  Execution halted

[mjsteinbaugh]

Seems like it's related to https://github.com/nf-core/rnaseq/blob/master/bin/salmon_tximport.r#L44

[drpatelh]

Hmmm...thats odd. The CI tests we use for the pipeline use -profile test,docker too and they have been passing. May be easier to get real-time help for these sorts of issues on the #rnaseq channel on nf-core Slack.

[drpatelh]

Did you manage to fix this @mjsteinbaugh ? Maybe worth re-running everything after tomorrow's release anyway.

[mjsteinbaugh]

@drpatelh I’ll recheck after the release update

[mjsteinbaugh]

Let's close for now, and I'll reopen if I'm still seeing issues