You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
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?
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
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
The text was updated successfully, but these errors were encountered: