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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` [exotic_engelbart] DSL2 - revision: 1344f41b7b
Downloading plugin [email protected]
[fd/ccc5cb] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[39/1ae779] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[35/e86e24] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[dd/af70af] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[b8/d2b57e] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[f5/f2813a] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[0e/5f04c1] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[ed/232aaf] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[b5/79b029] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[85/28b0d8] Submitted process > SRA:SRA_TO_SAMPLESHEET
[92/b43ffe] 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` [grave_albattani] DSL2 - revision: 1344f41b7b
[dd/59b267] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[a0/cdfc7a] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[de/e66dd9] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[01/181ef8] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[5b/265470] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[11/e841b7] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[b2/9e1c3e] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[4f/d0e425] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[e2/c12889] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[65/f5d45b] Submitted process > SRA:SRA_TO_SAMPLESHEET
[71/459932] 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` [pensive_heisenberg] DSL2 - revision: 1344f41b7b
[c7/5a4a7e] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[b5/566400] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[a5/7b8eb1] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[4a/b6df60] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[1a/593984] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[6b/5951a3] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[b1/139b9d] Submitted process > SRA:SRA_TO_SAMPLESHEET
[c1/fa82d7] 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` [pedantic_tuckerman] DSL2 - revision: 1344f41b7b
[ae/7e0f87] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[6e/f1c0b6] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[88/de9202] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[31/beea83] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[e4/4b698f] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[03/c17ba3] Submitted process > SRA:ASPERA_CLI (ERX1234253_ERR1160846)
[98/75902a] Submitted process > SRA:ASPERA_CLI (DRX026011_DRR028935)
[34/5ad58d] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[a0/770f4c] Submitted process > SRA:ASPERA_CLI (SRX6725035_SRR9984183)
[11/14bddb] Submitted process > SRA:SRA_TO_SAMPLESHEET
[fd/19515a] 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` [exotic_payne] DSL2 - revision: 1344f41b7b
[34/d77ffd] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[fa/fabdfe] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[17/8a0907] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[9f/5088b9] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[87/5119b9] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[39/84bad7] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[3c/3a3afa] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[cc/ba9854] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[06/54bc97] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[68/e84a1f] Submitted process > SRA:SRA_TO_SAMPLESHEET
[af/b4f6ae] 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` [pedantic_brenner] DSL2 - revision: 1344f41b7b
[14/bbc36c] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[53/fd0110] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[fc/e345d3] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[31/7628a6] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[df/8cd6f8] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[d7/32b9f2] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[de/511af6] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[ef/1be166] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[8d/f6764f] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[64/b6dd47] Submitted process > SRA:SRA_TO_SAMPLESHEET
[e8/3c7677] 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` [amazing_agnesi] DSL2 - revision: 1344f41b7b
[19/ed376f] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[e9/b7d982] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[aa/6f2192] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[19/d1d9ba] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[c1/9b41a5] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[42/a12e1b] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[30/0b3dbf] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[e4/c059af] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[24/b71ecb] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[af/72f6b8] Submitted process > SRA:SRA_TO_SAMPLESHEET
[33/446a5c] 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` [infallible_hodgkin] DSL2 - revision: 1344f41b7b
[99/cc0d56] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[27/0c5cd7] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[c5/d62bb4] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[4f/1e78a4] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[73/af9118] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[bb/8f2bd9] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[7c/c9fbb1] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[b4/217c3b] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[2c/4ee91d] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[ce/f0773b] Submitted process > SRA:SRA_TO_SAMPLESHEET
[00/ce366e] 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` [tender_colden] DSL2 - revision: 1344f41b7b
[48/a1d41e] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[2e/055586] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[08/e5f6ca] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[8d/4f19e1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[4b/d1ebab] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[14/3d3177] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[ad/f09ea1] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)
[01/8a50aa] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (ERR1160846)
[8e/8aff76] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (DRR028935)
[b2/c66d9a] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR9984183)
[39/137ae0] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (ERX1234253_ERR1160846)
[1e/f9c55a] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (DRX026011_DRR028935)
[86/0b417d] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX6725035_SRR9984183)
[66/3c2fd5] Submitted process > SRA:SRA_TO_SAMPLESHEET
[22/c8839a] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:
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