DSL2+ #312
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DSL2+ #312
GitHub Actions / JUnit Test Report
failed
Dec 10, 2024 in 0s
1 tests run, 0 passed, 0 skipped, 1 failed.
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Check failure on line 1 in Test pipeline
github-actions / JUnit Test Report
Test pipeline.Run with profile test
Assertion failed:
6 of 6 assertions failed
Raw output
Nextflow stdout:
N E X T F L O W ~ version 24.11.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/tests/../main.nf` [angry_franklin] DSL2 - revision: a82a3ad5a9
Downloading plugin [email protected]
WARN: WORKFLOW OUTPUT DSL IS A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
WARN: CHANNEL TOPICS ARE A PREVIEW FEATURE - SYNTAX AND FUNCTIONALITY CAN CHANGE IN FUTURE RELEASES
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/fetchngs 1.13.0dev[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/2732b911c57e607fa7aea5ba0c3d91b25bafb662/testdata/v1.12.0/sra_ids_test.csv[0m
[0;34moutdir : [0;32m/home/runner/work/fetchngs/fetchngs/~/tests/e1d0d533fa4114cdfd71d954f0715b76/output[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description: [0;32mMinimal test dataset to check pipeline function[0m
[1mGeneric options[0m
[0;34mtrace_report_suffix : [0;32m2024-12-10_17-02-11[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32mangry_franklin[0m
[0;34mcontainerEngine : [0;32mdocker[0m
[0;34mlaunchDir : [0;32m/home/runner/work/fetchngs/fetchngs/~/tests/e1d0d533fa4114cdfd71d954f0715b76[0m
[0;34mworkDir : [0;32m/home/runner/work/fetchngs/fetchngs/~/tests/e1d0d533fa4114cdfd71d954f0715b76/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/fetchngs/fetchngs[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-* The pipeline
https://doi.org/10.5281/zenodo.5070524
* The nf-core framework
https://doi.org/10.1038/s41587-020-0439-x
* Software dependencies
https://github.com/nf-core/fetchngs/blob/master/CITATIONS.md
WARN: Process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS > the `shell` block is deprecated, use `script` instead
WARN: Process NFCORE_FETCHNGS:SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH > the `shell` block is deprecated, use `script` instead
[8c/b4ccea] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR028935)
[22/d7e717] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR13191702)
[bf/284261] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (DRR026872)
[a0/099123] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR9984183)
[c4/703a61] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14593545)
[e7/b9f915] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR14709033)
[e7/48f93f] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (ERR1160846)
[70/e07b2d] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (SRR12848126)
[93/5ad6e3] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSM4907283)
[41/153414] Submitted process > NFCORE_FETCHNGS:SRA:SRA_IDS_TO_RUNINFO (GSE214215)
[fe/f5a735] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (1)
[bc/cda11a] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (2)
[62/f05c11] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (3)
[8f/201a96] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (4)
[f3/4453b5] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (5)
[94/daa235] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (6)
[7d/3ef45a] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (7)
[0d/eaf37b] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (8)
[2e/792535] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (9)
[63/8936f2] Submitted process > NFCORE_FETCHNGS:SRA:SRA_RUNINFO_TO_FTP (10)
[2d/00d467] Submitted process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[d8/1d9457] Submitted process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX9626017_SRR13191702)
[3e/7c84fc] Submitted process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (DRX024467_DRR026872)
[b8/8ff02c] Submitted process > NFCORE_FETCHNGS:SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
ERROR ~ Unexpected error [NullPointerException]
-- Check '/home/runner/work/fetchngs/fetchngs/~/tests/e1d0d533fa4114cdfd71d954f0715b76/meta/nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting
-- Check '/home/runner/work/fetchngs/fetchngs/~/tests/e1d0d533fa4114cdfd71d954f0715b76/meta/nextflow.log' file for details
WARN: Invalid extension 'yml' for index file '/home/runner/work/fetchngs/fetchngs/~/tests/e1d0d533fa4114cdfd71d954f0715b76/output/./nf_core_fetchngs_software_mqc_versions.yml' -- should be 'csv' or 'json'
-[0;35m[nf-core/fetchngs][0;31m Pipeline completed with errors[0m-
WARN: =============================================================================
Please double-check the samplesheet that has been auto-created by the pipeline.
Public databases don't reliably hold information such as strandedness
information, controls etc
All of the sample metadata obtained from the ENA has been appended
as additional columns to help you manually curate the samplesheet before
running nf-core/other pipelines.
===================================================================================
WARN: Killing running tasks (1)
Nextflow stderr:
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