Description of the bug

I specified an un-gzipped whitelist file with the --barcode_whitelist parameter. In the STAR_ALIGN step, it tries to unzip this file, which causes gzip to crash, which causes the step to fail. This is the offending line of .command.sh:

--soloCBwhitelist <(gzip -cdf 3M-february-2018.txt)

I will try to fix and submit a PR in the next day or two.

Command used and terminal output

$ nextflow run nf-core/scrnaseq
-profile singularity
--input ../samples.csv
--fasta: ../../ref/bGalGal1b_modified.fa
--gtf: ../../ref/bGalGal1b_modified_filtered.gtf
--protocol 10XV3
--aligner star
--outdir out
--barcode_whitelist /mnt/pixstor/data/esrbhb/3M-february-2018.txt
--save_reference

ERROR ~ Error executing process > 'NFCORE_SCRNASEQ:SCRNASEQ:STARSOLO:STAR_ALIGN (D2)'

Caused by:
Process NFCORE_SCRNASEQ:SCRNASEQ:STARSOLO:STAR_ALIGN (D2) terminated with an error exit status (104)

Command executed:

STAR
--genomeDir star
--readFilesIn D2_S2_L001_R2_001.fastq.gz D2_S2_L001_R1_001.fastq.gz
--runThreadN 16
--outFileNamePrefix D2.
--soloCBwhitelist <(gzip -cdf 3M-february-2018.txt)
--soloType CB_UMI_Simple
--soloFeatures Gene
--soloUMIlen 12

--sjdbGTFfile bGalGal1b_modified_genes.gtf
--outSAMattrRGline ID:D2 'SM:D2'

--readFilesCommand zcat --runDirPerm All_RWX --outWigType bedGraph --twopassMode Basic --outSAMtype BAM SortedByCoordinate \

if [ -f D2.Unmapped.out.mate1 ]; then
mv D2.Unmapped.out.mate1 D2.unmapped_1.fastq
gzip D2.unmapped_1.fastq
fi
if [ -f D2.Unmapped.out.mate2 ]; then
mv D2.Unmapped.out.mate2 D2.unmapped_2.fastq
gzip D2.unmapped_2.fastq
fi

if [ -d D2.Solo.out ]; then
# Backslashes still need to be escaped (nextflow-io/nextflow#67)
find D2.Solo.out ( -name ".tsv" -o -name ".mtx" ) -exec gzip {} ;
fi

cat <<-END_VERSIONS > versions.yml
"NFCORE_SCRNASEQ:SCRNASEQ:STARSOLO:STAR_ALIGN":
star: $(STAR --version | sed -e "s/STAR_//g")
END_VERSIONS

Command exit status:
104

Command output:
(empty)

Command error:
INFO: Environment variable SINGULARITYENV_TMPDIR is set, but APPTAINERENV_TMPDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_TASK_WORKDIR is set, but APPTAINERENV_NXF_TASK_WORKDIR is preferred
INFO: Environment variable SINGULARITYENV_NXF_DEBUG is set, but APPTAINERENV_NXF_DEBUG is preferred
gzip: invalid magic

EXITING because of FATAL ERROR: CB whitelist file /dev/fd/63 is empty.
SOLUTION: provide non-empty whitelist.

Oct 11 07:18:04 ...... FATAL ERROR, exiting

Work dir:
/mnt/pixstor/warrenwc-lab/users/edward/nxf_work/1a/6d24d1b3b8d570f7e134a16d877d51

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command.run

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details
-[nf-core/scrnaseq] Pipeline completed with errors-
WARN: Killing running tasks (1)

Relevant files

No response

System information

• Nextflow version: 24.04.3
• nf-core/scrnaseq version: v2.7.1-g4171377
• slurm executor
• singularity profile
• CentOS