A bug appears when I tested the pipeline.
Command:
nextflow run nf-core/spatialtranscriptomics -profile test,docker -r dev
N E X T F L O W ~ version 22.04.5
Launching `https://github.com/nf-core/spatialtranscriptomics` [amazing_wescoff] DSL2 - revision: 40e2fe8125 [dev]
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nf-core/spatialtranscriptomics v1.0dev
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Core Nextflow options
revision : dev
runName : amazing_wescoff
containerEngine : docker
launchDir : /home/jmh/tmp
workDir : /home/jmh/tmp/work
projectDir : /home/jmh/.nextflow/assets/nf-core/spatialtranscriptomics
userName : jmh
profile : test,docker
configFiles : /home/jmh/.nextflow/assets/nf-core/spatialtranscriptomics/nextflow.config
Input/output options
input : https://raw.githubusercontent.com/nf-core/test-datasets/spatialtranscriptomics/testdata/test-dataset-subsampled/samplesheet.csv
Institutional config options
config_profile_name : Test profile
config_profile_description: Minimal test dataset to check pipeline function
Max job request options
max_cpus : 4
max_memory : 6.GB
max_time : 1.h
!! Only displaying parameters that differ from the pipeline defaults !!
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If you use nf-core/spatialtranscriptomics for your analysis please cite:
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/spatialtranscriptomics/blob/master/CITATIONS.md
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Project directory: /home/jmh/.nextflow/assets/nf-core/spatialtranscriptomics
Module compilation error
- file : /home/jmh/.nextflow/assets/nf-core/spatialtranscriptomics/./workflows/../subworkflows/local/../../modules/local/tasks.nf
- cause: unable to resolve class JsonSlurper
@ line 201, column 19.
sample_info = new JsonSlurper().parse(new File(fileName))
^
Module compilation error
- file : /home/jmh/.nextflow/assets/nf-core/spatialtranscriptomics/./workflows/../subworkflows/local/../../modules/local/tasks.nf
- cause: unable to resolve class JsonSlurper
@ line 339, column 19.
sample_info = new JsonSlurper().parse(new File(fileName))
^
2 errors
### Relevant files
_No response_
### System information
- Nextflow version: 22.04.5
- Container engine: Docker
- OS: CentOS Linux
- Version of nf-core/spatialtranscriptomics: dev