Does the --no-container work?

[qiyubio]

Hi, my command line with "--singularity" works great:

cwltool --singularity --tmp-outdir-prefix=/lscratch/$SLURM_JOB_ID/ \
--tmpdir-prefix=/lscratch/$SLURM_JOB_ID/ \
$VIRTUS_WORKFLOW/VIRTUS.PE.cwl \
--fastq1 ERR3240275_1.fastq.gz --fastq2 ERR3240275_2.fastq.gz \
--genomeDir_human $VIRTUS_INDEX/STAR_index_human \
--genomeDir_virus $VIRTUS_INDEX/STAR_index_virus \
--salmon_index_human $VIRTUS_INDEX/salmon_index_human \
--salmon_quantdir_human salmon_human \
--nthreads 40

But when I switch "--singularity" to "--no-container", it failed with this error:

ERROR Exception on step 'fastp_pe'
ERROR [step fastp_pe] Cannot make job: --no-container, but this CommandLineTool has DockerRequirement under 'requirements'.

Fastp was installed. Any thought?

[yyoshiaki]

Thank you for trying our tool and report the issue. You are definitely right. We will remove the --no-container indication from Wiki.