failed to run nextflow command

[ryao-mdanderson]

Operating System

Other Linux (please specify below)

Other Linux

RHEL8.7

Workflow Version

23.10.0

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-clone-validation –help

Workflow Execution - CLI Execution Profile

None

What happened?

nextflow run epi2me-labs/wf-clone-validation –help

the error message is ERROR ~ Validation of pipeline parameters failed! -- Check '.nextflow.log' file for details ERROR ~ * Missing required parameter: --fastq -- Check '.nextflow.log' file for details

Relevant log output

$ module list

Currently Loaded Modules:
  1) openjdk/17.0.3+7   2) nextflow/23.10.0

[ryao@ldragon4 epi2me-labs]$ nextflow run epi2me-labs/wf-clone-validation –help
CAPSULE: Downloading dependency org.codehaus.groovy:groovy:jar:3.0.19
CAPSULE: Downloading dependency io.nextflow:nf-httpfs:jar:23.10.0
CAPSULE: Downloading dependency io.nextflow:nf-commons:jar:23.10.0
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-xml:jar:3.0.19
CAPSULE: Downloading dependency org.slf4j:log4j-over-slf4j:jar:2.0.7
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-annotations:jar:2.14.2
CAPSULE: Downloading dependency org.eclipse.jgit:org.eclipse.jgit:jar:6.5.0.202303070854-r
CAPSULE: Downloading dependency org.slf4j:slf4j-api:jar:2.0.7
CAPSULE: Downloading dependency org.slf4j:jul-to-slf4j:jar:2.0.7
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-core:jar:2.14.2
CAPSULE: Downloading dependency com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:jar:2.14.2
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-json:jar:3.0.19
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-templates:jar:3.0.19
CAPSULE: Downloading dependency ch.qos.logback:logback-core:jar:1.4.6
CAPSULE: Downloading dependency org.slf4j:jcl-over-slf4j:jar:2.0.7
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-yaml:jar:3.0.19
CAPSULE: Downloading dependency ch.qos.logback:logback-classic:jar:1.4.6
CAPSULE: Downloading dependency org.codehaus.groovy:groovy-nio:jar:3.0.19
CAPSULE: Downloading dependency io.nextflow:nextflow:jar:23.10.0
CAPSULE: Downloading dependency com.fasterxml.jackson.core:jackson-databind:jar:2.14.2
Nextflow 23.10.1 is available - Please consider updating your version to it
N E X T F L O W  ~  version 23.10.0
Pulling epi2me-labs/wf-clone-validation ...
 downloaded from https://github.com/epi2me-labs/wf-clone-validation.git
Launching `https://github.com/epi2me-labs/wf-clone-validation` [focused_curran] DSL2 - revision: 2c04b9d884 [master]

ERROR ~ Validation of pipeline parameters failed!

 -- Check '.nextflow.log' file for details
ERROR ~ * Missing required parameter: --fastq

 -- Check '.nextflow.log' file for details

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

I also tried running with demo data, 

$ export NXF_SINGULARITY_CACHEDIR="${HOME}/singularity"
$ export DEMODATA="/rsrch3/scratch/reflib/REFLIB_data/wf-clone-validation-1.2.0"
 -- I downloaded demo data in above location.

$ date; nextflow run epi2me-labs/wf-clone-validation \
>  --fastq $DEMODATA/clone_val_test/fastq --primers $DEMODATA/clone_val_test/primers.tsv \
>  --host_reference $DEMODATA/clone_val_test/host_reference.fa.gz --regions_bedfile $DEMODATA/clone_val_test/reference.bed \
>  --insert_reference $DEMODATA/clone_val_test/insert_reference.fasta --sample_sheet $DEMODATA/clone_val_test/sample_sheet.csv \
>  -profile singularity -without-docker

seeing output
Mon Mar 11 17:09:46 CDT 2024
CAPSULE: Downloading dependency org.multiverse:multiverse-core:jar:0.7.0
CAPSULE: Downloading dependency org.apache.ivy:ivy:jar:2.5.1
.....

until hit an error :
ERROR ~ Error executing process > 'pipeline:medakaVersion'
Caused by:
Failed to pull singularity image
command: singularity pull --name ontresearch-medaka-sha61a9438d745a78030738352e084445a2db3daa2a.img.pulling.1710195000442 docker://ontresearch/medaka:sha61a9438d745a78030738352e084445a2db3daa2a > /dev/null
status : 255
...
FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: no descriptor found for reference "3290aa3a218b2b5b4e77cfeb367d91827f32ea827cc90219e723b00a6fb6f490"
issue report to github

[ryao-mdanderson]

Dear author,

Any suggestion? Please let me know if you need more information.

Thanks!

[sarahjeeeze]

Hi, for help its just a double dash --help, and when you try to run it looks like a singularity issue. You might find this blog post useful https://labs.epi2me.io/singularity/ - Does singularity work for you independently of running the workflow?

[sarahjeeeze]

Closing through lack of response.