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yyoshiaki / VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
https://github.com/yyoshiaki/VIRTUS/wiki
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Does the --no-container work? #26

Closed qiyubio closed 3 years ago

qiyubio commented 3 years ago

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 commented 3 years ago

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