I am running a dropseq generated library through nf-core/scrnaseq pipeline and the starSolo errors with the following:

Command exit status:
  2

Command output:
  (empty)

Command error:
  INFO:    Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
  INFO:    Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
  .command.sh: line 2: conditional binary operator expected

Here is the .command.sh lines (including the offending line 2):

#!/usr/bin/env bash -C -e -u -o pipefail
if [[  == *.gz ]]; then
    gzip -cdf  > whitelist.uncompressed.txt
else
    cp  whitelist.uncompressed.txt
fi

STAR \
    --genomeDir star \
    --readFilesIn MFI121_cs12_S1_L001_R2_001.fastq.gz MFI121_cs12_S1_L001_R1_001.fastq.gz \
    --runThreadN 12 \
    --outFileNamePrefix MFI121_cs12_S1_L001. \
    --soloCBwhitelist whitelist.uncompressed.txt \
    --soloType SmartSeq \
    --soloFeatures Gene \
     \
     \
    --sjdbGTFfile Macaca_fascicularis.Macaca_fascicularis_6.0.dna.toplevel_genes.gtf \
    --outSAMattrRGline ID:MFI121_cs12_S1_L001 'SM:MFI121_cs12_S1_L001' \
     \
    --readFilesCommand zcat --runDirPerm All_RWX --outWigType bedGraph --twopassMode Basic --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 77309411328 \

On BioStars I found that there is not appropriate white barcode list to be be provided and --soloCBwhitelist None is used instead (https://www.biostars.org/p/431806/). Is None an acceptable with --barcode-whitelist?

Hey, there are currently two open PRs that tackle this: • #486 • #488 However, nothing happened there for a while. @Gregor Sturm in #486 you said you have to think about how to harmonize them, any update there? Otherwise I can have a look

Hi Nico, if you have time to look into it, feel free to do to these PRs whatever you think is best