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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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/2599673342ff43612ff5d2c71e6538ee/meta/mock.nf` [fabulous_hoover] DSL2 - revision: 1344f41b7b
Downloading plugin [email protected]
[24/e3b252] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[c2/3b1f91] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[21/82657e] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[63/414536] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[48/2684ae] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[3c/466fcd] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[97/739cd1] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[7a/2fae53] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[4f/d8b9ff] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[94/dd6cfc] Submitted process > SRA:SRA_TO_SAMPLESHEET
[f1/b0e71f] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/8b973ab156599d87f83112471195810d/meta/mock.nf` [astonishing_williams] DSL2 - revision: 1344f41b7b
[72/1ed8c0] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[96/cdf8a8] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[c5/fb9545] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[54/ac6a4e] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[90/c7a155] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[ed/013fbd] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[1a/d78635] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[34/556a42] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[df/a2f79f] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[65/41873b] Submitted process > SRA:SRA_TO_SAMPLESHEET
[52/d993de] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3d6393be2180a31d0d4eaf50b073261/meta/mock.nf` [chaotic_sammet] DSL2 - revision: 1344f41b7b
[f0/99fabf] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[1b/a48c08] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[5b/3481a7] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[ca/1a34e1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[66/cfb106] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[60/fe7776] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[6c/1db3e1] Submitted process > SRA:SRA_TO_SAMPLESHEET
[3a/92464b] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/fb74b37e9342216c448289729f5f970d/meta/mock.nf` [loving_ardinghelli] DSL2 - revision: 1344f41b7b
[2b/4d440e] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[59/269f2b] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[97/15d7e9] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[04/4546e6] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[ff/14cfa1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[32/8dbb00] Submitted process > SRA:ASPERA_CLI (ERX1234253_ERR1160846)
[4b/bd7fbc] Submitted process > SRA:ASPERA_CLI (DRX026011_DRR028935)
[a5/7b37d1] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[a3/acd3d3] Submitted process > SRA:ASPERA_CLI (SRX6725035_SRR9984183)
[9a/7b2521] Submitted process > SRA:SRA_TO_SAMPLESHEET
[c5/ca5a13] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/b6119d1bc44a05070663cabe6d10e8c3/meta/mock.nf` [grave_kare] DSL2 - revision: 1344f41b7b
[53/ac1723] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[40/d27342] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[a0/16b047] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[67/b52689] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[7b/eb54d6] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[7c/adf35f] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[a7/4ed834] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[98/a6d2a2] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[c1/0374b4] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[67/bd8425] Submitted process > SRA:SRA_TO_SAMPLESHEET
[5f/d9cef1] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/7c7c71c862b2f925a2446f34a598cef7/meta/mock.nf` [naughty_brazil] DSL2 - revision: 1344f41b7b
[c7/fc2e42] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[f9/66e582] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[08/5db1b8] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[79/b8674a] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[8a/ca7f5f] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[d2/c0652c] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[ea/447311] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[90/d36dec] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[94/040615] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[80/f06ca0] Submitted process > SRA:SRA_TO_SAMPLESHEET
[32/1f4274] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/373310d47d878172dd887ebfbc32cceb/meta/mock.nf` [lethal_ride] DSL2 - revision: 1344f41b7b
[be/05ac5d] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[db/157d93] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[2c/658724] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[f9/58e59c] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[83/3e06ca] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[35/1256ca] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[05/5543db] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[cb/00f5b9] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[40/b87309] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[c4/e37866] Submitted process > SRA:SRA_TO_SAMPLESHEET
[e8/1152bf] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/cbeb2a3299add8cdc56b0eebd95d2296/meta/mock.nf` [golden_franklin] DSL2 - revision: 1344f41b7b
[2c/717b49] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[49/f9adb3] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[15/5b606b] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[9e/14610a] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[03/776bba] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[6c/3adc97] Submitted process > SRA:SRA_FASTQ_FTP (SRX6725035_SRR9984183)
[39/b40e17] Submitted process > SRA:SRA_FASTQ_FTP (ERX1234253_ERR1160846)
[37/1c8faf] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[c7/fd5e32] Submitted process > SRA:SRA_FASTQ_FTP (DRX026011_DRR028935)
[0a/5ac5df] Submitted process > SRA:SRA_TO_SAMPLESHEET
[9a/8733d3] 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 24.01.0-edge
Launching `/home/runner/work/fetchngs/fetchngs/~/tests/a3f98fa2447097ae52f7f0c28c9fd2e5/meta/mock.nf` [nasty_volhard] DSL2 - revision: 1344f41b7b
[91/c0a0b1] Submitted process > SRA:SRA_IDS_TO_RUNINFO (ERX1234253)
[04/26ca66] Submitted process > SRA:SRA_IDS_TO_RUNINFO (DRX026011)
[88/cfd9ce] Submitted process > SRA:SRA_IDS_TO_RUNINFO (SRX6725035)
[aa/d0ca98] Submitted process > SRA:SRA_RUNINFO_TO_FTP (1)
[26/c50f18] Submitted process > SRA:SRA_RUNINFO_TO_FTP (2)
[6f/50ce4f] Submitted process > SRA:SRA_RUNINFO_TO_FTP (3)
[a8/0e5df7] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:CUSTOM_SRATOOLSNCBISETTINGS (ncbi-settings)
[fc/ffa318] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (DRR028935)
[f0/ca20cf] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (SRR9984183)
[35/7a3c15] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_PREFETCH (ERR1160846)
[37/eea836] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (DRX026011_DRR028935)
[8a/0f8a84] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (SRX6725035_SRR9984183)
[17/c337f0] Submitted process > SRA:FASTQ_DOWNLOAD_PREFETCH_FASTERQDUMP_SRATOOLS:SRATOOLS_FASTERQDUMP (ERX1234253_ERR1160846)
[2d/b5901a] Submitted process > SRA:SRA_TO_SAMPLESHEET
[d3/98fc35] Submitted process > SRA:MULTIQC_MAPPINGS_CONFIG
Nextflow stderr:
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