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Organize into subworkflows #59

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Organize into subworkflows #59

fix prettier
c4603b5
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GitHub Actions / JUnit Test Report failed Dec 20, 2023 in 0s

20 tests run, 3 passed, 0 skipped, 17 failed.

Annotations

Check failure on line 1 in Single-Read

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Single-Read 

Assertion failed: 

5 of 5 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/c76a64f80627589a76854a3c00272f08/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Paired-Reads

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Paired-Reads 

Assertion failed: 

6 of 6 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/3ca5cad20e495dbc56420483ff0750d3/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in MULTIQC: FASTQC

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

MULTIQC: FASTQC 

Assertion failed: 

4 of 4 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/66fe40f57c85e960c841665f04b2cac6/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in MULTIQC: FASTQC and a config file

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

MULTIQC: FASTQC and a config file 

Assertion failed: 

4 of 4 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/ed8961d0dfaa2c5360b9bcc896808a40/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in test_samtools_sort

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_samtools_sort 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/5586ee536cc61ab5bca7b712cb6b9828/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in test_samtools_sort_stub

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

test_samtools_sort_stub 

Assertion failed: 

2 of 2 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/14ef62cf6ca4a0d830842fa51502cb8/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in sarscov2 [BAI]

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

sarscov2 [BAI] 

Assertion failed: 

3 of 3 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 33 or see '/tmp/tests/20994b0114282f866d1890b14d593647/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens [CRAI]

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens [CRAI] 

Assertion failed: 

3 of 3 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script 'meta/mock.nf' at line: 33 or see '/tmp/tests/8d270200434bcdbaefe7dfb949574ec0/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens [CSI]

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens [CSI] 

Assertion failed: 

3 of 3 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 33 or see '/tmp/tests/e89428d19e05a82d286b5941b7c1bee3/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in Should run without failures

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Should run without failures 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

WARN: There's no process matching config selector: FASTQC
WARN: There's no process matching config selector: STAR_ALIGN_HOST
WARN: There's no process matching config selector: STAR_ALIGN_PLUS
WARN: There's no process matching config selector: STAR_ALIGN_VALIDATE
WARN: There's no process matching config selector: TRIMMOMATIC
Nextflow stderr:

Check failure on line 1 in Single-Read

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Single-Read 

Assertion failed: 

5 of 5 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'sarscov2' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/9bafc5d01a83f6d41a23c76e3aa66d64/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens - single_end

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens - single_end 

Assertion failed: 

17 of 17 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/53ba1b41ab864d3c8cf37ad9c035aa7f/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens - paired_end

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens - paired_end 

Assertion failed: 

17 of 17 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/326f8a0ac43d1ae05ac44b0dee53806b/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens - paired_end - arriba

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens - paired_end - arriba 

Assertion failed: 

17 of 17 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/163f9476331594abf3402dfe641c139f/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens - paired_end - starfusion

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens - paired_end - starfusion 

Assertion failed: 

17 of 17 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/285386c973f6855c9f98d58c4da35cf4/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens - paired_end - multiple

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens - paired_end - multiple 

Assertion failed: 

17 of 17 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script 'meta/mock.nf' at line: 34 or see '/tmp/tests/1eb846bb10bf1a5317a083727e7b61d7/meta/nextflow.log' file for more details
Nextflow stderr:

Check failure on line 1 in homo_sapiens

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

homo_sapiens 

Assertion failed: 

3 of 3 assertions failed
Raw output 
Nextflow stdout:

WARN: Access to undefined parameter `test_data` -- Initialise it to a default value eg. `params.test_data = some_value`
ERROR ~ Cannot get property 'homo_sapiens' on null object

 -- Check script 'meta/mock.nf' at line: 33 or see '/tmp/tests/426becc6241ba2ab572e343844d5b452/meta/nextflow.log' file for more details
Nextflow stderr:
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