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Workflow output definition #963

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Workflow output definition

Workflow output definition #963

GitHub Actions / JUnit Test Report failed Feb 28, 2024 in 0s

10 tests run, 1 passed, 0 skipped, 9 failed.

Annotations

Check failure on line 1 in Parameters: --nf_core_pipeline rnaseq

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline rnaseq 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/2599673342ff43612ff5d2c71e6538ee/meta/mock.nf` [angry_torvalds] DSL2 - revision: 1344f41b7b
Downloading plugin [email protected]
[2a/4a05d7] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[45/5794dd] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[b2/5ecb7a] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[38/da55cb] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[f2/61194b] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[36/f00550] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[57/f73485] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[dc/c4cb79] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[ca/9f4b6b] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[7c/43f919] Submitted process > SRA:SRA_TO_SAMPLESHEET
[ee/1f5c53] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in .devcontainer

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

.Parameters: --nf_core_pipeline rnaseq --ena_metadata_fields ... --sample_mapping_fields ... 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/8b973ab156599d87f83112471195810d/meta/mock.nf` [awesome_galileo] DSL2 - revision: 1344f41b7b
[de/a030e9] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[de/eec1c5] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[2a/1b1f84] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[ca/c6c56a] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[f0/fddad9] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[52/fb68a2] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[68/bb83d5] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[48/51abf1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[e4/ece657] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[4d/3aa3e8] Submitted process > SRA:SRA_TO_SAMPLESHEET
[ea/3786f2] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --skip_fastq_download

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --skip_fastq_download 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3d6393be2180a31d0d4eaf50b073261/meta/mock.nf` [extravagant_curie] DSL2 - revision: 1344f41b7b
[ef/9267b3] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[17/f2081d] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[02/6eedd3] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[44/16d85a] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[d6/4c420c] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[e6/ae7640] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[1e/b71c6f] Submitted process > SRA:SRA_TO_SAMPLESHEET
[a7/74bc73] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --download_method aspera

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --download_method aspera 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/fb74b37e9342216c448289729f5f970d/meta/mock.nf` [curious_kay] DSL2 - revision: 1344f41b7b
[98/9f872b] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[f3/e7dd46] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[2b/f188fd] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[32/9b6d2a] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[10/26fcd5] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[84/82883a] Submitted process > SRA:ASPERA_CLI (SRX6725035_SRR9984183)
[20/0ee30f] Submitted process > SRA:ASPERA_CLI (ERX1234253_ERR1160846)
[61/1c5bc1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[1e/b92b33] Submitted process > SRA:ASPERA_CLI (DRX026011_DRR028935)
[8c/5afae9] Submitted process > SRA:SRA_TO_SAMPLESHEET
[cd/027aad] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --nf_core_pipeline viralrecon

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline viralrecon 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/b6119d1bc44a05070663cabe6d10e8c3/meta/mock.nf` [clever_gutenberg] DSL2 - revision: 1344f41b7b
[d7/4907b6] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[8b/370c01] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[fb/eb893a] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[53/b9c63b] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[67/55e76c] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[86/5e0e1f] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[c8/1ff642] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[55/7abed7] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[18/95814d] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[59/a2609d] Submitted process > SRA:SRA_TO_SAMPLESHEET
[e1/585536] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --nf_core_pipeline atacseq

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline atacseq 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/7c7c71c862b2f925a2446f34a598cef7/meta/mock.nf` [marvelous_cantor] DSL2 - revision: 1344f41b7b
[ee/99b7eb] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[20/4ca781] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[e4/983aca] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[6a/052ed5] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[bc/fcc3ab] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[2e/52b8db] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[22/07263d] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[05/5ea74f] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[d0/5fc5a4] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[33/52d925] Submitted process > SRA:SRA_TO_SAMPLESHEET
[77/7647d0] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --nf_core_pipeline taxprofiler

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --nf_core_pipeline taxprofiler 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/373310d47d878172dd887ebfbc32cceb/meta/mock.nf` [pensive_brenner] DSL2 - revision: 1344f41b7b
[46/bb8cf3] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[6d/7989a1] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[4c/943a40] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[7b/f4dd37] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[33/6012e1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[4e/0d0d67] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[2b/6db239] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[9f/0946c6] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[84/e6f786] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[e5/cb0c50] Submitted process > SRA:SRA_TO_SAMPLESHEET
[17/f705b0] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: default

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: default 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/cbeb2a3299add8cdc56b0eebd95d2296/meta/mock.nf` [spontaneous_ride] DSL2 - revision: 1344f41b7b
[6d/74051a] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[35/3f6948] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[40/dedeff] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[83/c8868e] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[d2/d9dd56] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[9a/d6a56d] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[7e/6b908c] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[1e/7adbe9] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[51/26c7e6] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[ba/cc59f1] Submitted process > SRA:SRA_TO_SAMPLESHEET
[a7/64eca9] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:

Check failure on line 1 in Parameters: --download_method sratools

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Parameters: --download_method sratools 

Assertion failed: 

2 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.5
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3f98fa2447097ae52f7f0c28c9fd2e5/meta/mock.nf` [golden_tesla] DSL2 - revision: 1344f41b7b
[9b/6fcb49] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[61/df9c9f] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[ce/f7c828] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[40/0d0dce] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[c7/939efd] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[a7/b1abb1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[65/275897] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)
[ec/fda426] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (DRR028935)
[b9/a9063c] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR9984183)
[fb/7918a0] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (ERR1160846)
[81/3d6982] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (DRX026011_DRR028935)
[cc/1ccff9] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX6725035_SRR9984183)
[2c/feb92c] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (ERX1234253_ERR1160846)
[81/fa775a] Submitted process > SRA:SRA_TO_SAMPLESHEET
[75/061180] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:
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