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Remove existing tests that are duplicated by PUBLISH_GENOME tests #15

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Remove existing tests that are duplicated by PUBLISH_GENOME tests

Remove existing tests that are duplicated by PUBLISH_GENOME tests #15

GitHub Actions / JUnit Test Report failed Mar 12, 2024 in 0s

22 tests run, 4 passed, 0 skipped, 18 failed.

Annotations

Check failure on line 1 in default options

@github-actions github-actions / JUnit Test Report

default options 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/4922e1257927ccf685775ee9d0a7280/meta/mock.nf` [silly_einstein] DSL2 - revision: 16f4c80bf2
Downloading plugin [email protected]
Downloading plugin [email protected]
[47/1415c5] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[4b/5a4347] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[5e/614fab] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[27/db320b] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ab/2acea4] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gencode = false

@github-actions github-actions / JUnit Test Report

gencode = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/df6e2f3b6eb1e7495a70f3876a9989f8/meta/mock.nf` [gigantic_koch] DSL2 - revision: 4ee6ac0879
[b2/c0125c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[69/4b19a0] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[b4/ff1b84] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[fc/0da907] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[d4/b2e820] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_gtf_filter

@github-actions github-actions / JUnit Test Report

skip_gtf_filter 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/f339e851a286ff522c3e0beb50fe3be1/meta/mock.nf` [nasty_hawking] DSL2 - revision: e7f5379587
[25/62e24f] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[f2/f28e2c] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[72/0cc47c] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[35/db0aa1] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_alignment

@github-actions github-actions / JUnit Test Report

skip_alignment 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/3c61ffe84901e224f8596162369fa16b/meta/mock.nf` [fabulous_gates] DSL2 - revision: 841b65a2c4
[ea/eee0f2] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[a6/dffdb3] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[37/f56e59] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[30/f2a214] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[c1/c8570c] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_psuedo_alignment

@github-actions github-actions / JUnit Test Report

skip_psuedo_alignment 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/ef4cf09b6b5d841d2b83ebc9b293b79b/meta/mock.nf` [astonishing_kimura] DSL2 - revision: cb7820872d
[fc/d39f38] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[84/c1d65f] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[b2/d7182d] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[1f/2328b8] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[4d/7f256e] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gtf = false

@github-actions github-actions / JUnit Test Report

gtf = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/31cd6fc1f2b87508d056f0576a47414f/meta/mock.nf` [maniac_pare] DSL2 - revision: 38988486f6
[a7/fd0b9e] Submitted process > PREPARE_GENOME:GFFREAD (genes.gff)
[69/c56374] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[6a/600734] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[fb/60ac79] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[89/150ebf] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[6c/34ee60] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[a6/da27a8] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gff = false

@github-actions github-actions / JUnit Test Report

gff = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/c8f05ee08b0cdfa1ee9b9bc96740c6dd/meta/mock.nf` [amazing_banach] DSL2 - revision: bd058f72cb
[da/0919fe] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[08/15a82b] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[72/c77bfa] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[43/2d6b3c] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[41/e1f8f8] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gfp = false

@github-actions github-actions / JUnit Test Report

gfp = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/69623ba3968fbec40b61a152416ddbfe/meta/mock.nf` [amazing_raman] DSL2 - revision: 99644d12ee
[a8/cad914] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
[fe/50cb41] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fasta)
[3f/2cec6d] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[8d/095452] Submitted process > PREPARE_GENOME:GTF2BED (genome.filtered.gtf)
Nextflow stderr:

Check failure on line 1 in transcriptome = false

@github-actions github-actions / JUnit Test Report

transcriptome = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/51902a0f751bc26567a1ba31abd4911a/meta/mock.nf` [angry_hawking] DSL2 - revision: 28200cf32c
[e0/37bacc] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[d4/748f91] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[cc/7f8a38] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[01/b47712] Submitted process > PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome_gfp.fasta)
[c4/4e841d] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[26/318ce2] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in with bed

@github-actions github-actions / JUnit Test Report

with bed 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/b398835a950609c8c0ca270c809fd9c2/meta/mock.nf` [golden_ekeblad] DSL2 - revision: 8e5af7d742
[a0/99e6cf] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[59/a5e7ea] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[a3/315c25] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[55/b81a70] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in rsem_index = false

@github-actions github-actions / JUnit Test Report

rsem_index = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/1cd609e2d9c3c55976d7a9c31b7386f1/meta/mock.nf` [compassionate_einstein] DSL2 - revision: cf5e67199b
[b9/6af86a] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[e7/97d504] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[9b/6ad50c] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[5f/bfd7b0] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[cc/0b38d5] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in salmon_index = false

@github-actions github-actions / JUnit Test Report

salmon_index = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/f144c13216129855be97ab2789fa0e51/meta/mock.nf` [shrivelled_jones] DSL2 - revision: 5630400e88
[ab/c01670] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[ee/a78914] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[b6/155e72] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[f0/6f39ce] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[14/0f27e7] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in hisat2_index = false

@github-actions github-actions / JUnit Test Report

hisat2_index = false 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/9db6722ba8b5f29ab0f51f62207cc9fb/meta/mock.nf` [shrivelled_shirley] DSL2 - revision: 97a73ef989
[c4/d2a86b] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[a0/70dac3] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[6c/d88851] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ac/6a2d4c] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[a7/b51d62] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gencode = true

@github-actions github-actions / JUnit Test Report

gencode = true 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/31283685ab30eae30a35c1463e2e4348/meta/mock.nf` [golden_lavoisier] DSL2 - revision: bd6a5cf449
[f1/b77bcd] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[4f/7f6530] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[89/8b735a] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[6d/71381e] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ff/4563dc] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[36/6bf82f] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in featurecounts_group_type = 'gene_type'

@github-actions github-actions / JUnit Test Report

featurecounts_group_type = 'gene_type' 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/6626e6f5929ac7ca6a968b65d0d9c2e6/meta/mock.nf` [cranky_ritchie] DSL2 - revision: 3e1d4d30c5
[c0/8d3a24] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[04/06b36e] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[42/6b1057] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[6b/10ce14] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[11/38e567] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_gtf_filter = true

@github-actions github-actions / JUnit Test Report

skip_gtf_filter = true 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/162c18380fbc5b48ce6831fe0fe8dbde/meta/mock.nf` [silly_goldberg] DSL2 - revision: e7f5379587
[f5/bc793a] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[87/730794] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[c8/f51475] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[ef/66fb29] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_alignment = true

@github-actions github-actions / JUnit Test Report

skip_alignment = true 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/ad6917857702638153a6acb462865b8a/meta/mock.nf` [compassionate_kowalevski] DSL2 - revision: 841b65a2c4
[e7/9e63cb] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[36/42f5a5] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[b1/6a9e4b] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[a5/31341f] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[4b/43b7ee] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_pseudoalignment = true

@github-actions github-actions / JUnit Test Report

skip_pseudoalignment = true 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 23.04.0
Launching `/home/runner/work/rnaseq/rnaseq/~/tests/46ca2375c42e67b455434c3de4e5e5c4/meta/mock.nf` [goofy_archimedes] DSL2 - revision: cb7820872d
[d7/a3da5f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[34/1564e4] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[cc/a95eea] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[cd/6b7a5e] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[54/e4d808] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:
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