Remove existing tests that are duplicated by PUBLISH_GENOME tests · adamrtalbot/rnaseq@7aeb72d · GitHub

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

36 tests run, 18 passed, 0 skipped, 18 failed.

Annotations

Check failure on line 1 in default options

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` [cheesy_liskov] DSL2 - revision: 16f4c80bf2
Downloading plugin [email protected]
Downloading plugin [email protected]
[e2/385513] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[a6/bce748] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[95/1bf363] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[f8/166e64] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[e0/343425] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gencode = false

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` [soggy_mercator] DSL2 - revision: 4ee6ac0879
[c8/d6af10] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[18/008613] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[7f/ea3194] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[bd/0a42da] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[e0/5a1b68] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_gtf_filter

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` [nauseous_newton] DSL2 - revision: e7f5379587
[69/f8b268] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[c9/ade980] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[7d/f30fe1] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[9b/5508da] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_alignment

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` [marvelous_kay] DSL2 - revision: 841b65a2c4
[76/4e66d7] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[23/7c74d1] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[ae/57cfc9] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[bb/8e4de4] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[15/a20449] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_psuedo_alignment

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` [prickly_elion] DSL2 - revision: cb7820872d
[58/dfaf0f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[21/10eae8] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[b1/aca1f6] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[08/f2369f] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[c6/67285d] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gtf = false

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` [compassionate_morse] DSL2 - revision: 38988486f6
[d4/b8ff74] Submitted process > PREPARE_GENOME:GFFREAD (genes.gff)
[eb/b74402] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[16/2ad82f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[4d/1e872f] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[6f/bc9f96] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[46/6c14aa] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[a4/21a9b6] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gff = false

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` [cheeky_khorana] DSL2 - revision: bd058f72cb
[6d/ac25a3] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[4d/39e69f] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[1f/a17678] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ce/b0c88c] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[01/8f26cb] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gfp = false

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` [crazy_hopper] DSL2 - revision: 99644d12ee
[31/714f8f] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fasta)
[3b/fe1211] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
[ac/15232b] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[c5/728b1f] Submitted process > PREPARE_GENOME:GTF2BED (genome.filtered.gtf)
Nextflow stderr:

Check failure on line 1 in transcriptome = false

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` [disturbed_khorana] DSL2 - revision: 28200cf32c
[3c/9d197c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[01/8b2796] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[cd/bb6c9f] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[3a/c6fce0] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[6b/94e81e] Submitted process > PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome_gfp.fasta)
[ac/a751f2] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in with bed

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` [friendly_woese] DSL2 - revision: 8e5af7d742
[33/82e4c6] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[b6/635008] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[d7/fe0cb9] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[c0/b9c8ed] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in rsem_index = false

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` [magical_planck] DSL2 - revision: cf5e67199b
[89/4c220f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[5f/f43a4d] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[c2/78d60b] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[38/abc76d] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[98/4b026f] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in salmon_index = false

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` [compassionate_neumann] DSL2 - revision: 5630400e88
[5d/e8abf0] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[e3/2c6baa] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[6d/c998c1] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[8e/46628e] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[fe/62cc40] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in hisat2_index = false

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` [peaceful_mirzakhani] DSL2 - revision: 97a73ef989
[20/301e44] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[00/b6fbdc] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[d1/8fe9e0] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[fe/7b92cb] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[85/876a99] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in gencode = true

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` [elated_mendel] DSL2 - revision: bd6a5cf449
[88/031db0] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[fa/b35cfe] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[16/861ab2] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[cc/0e1296] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[36/64f20e] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[0a/facca5] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in featurecounts_group_type = 'gene_type'

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` [curious_faraday] DSL2 - revision: 3e1d4d30c5
[8c/de8e6d] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[d2/f4319d] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[5d/027cfb] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[16/3fe19b] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[07/3fe0b8] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_gtf_filter = true

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` [mighty_northcutt] DSL2 - revision: e7f5379587
[49/ecf5db] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[36/067b46] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[c0/12dfaa] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[0c/f96f2f] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_alignment = true

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` [voluminous_bernard] DSL2 - revision: 841b65a2c4
[01/1f5e81] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[c9/35bdd7] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[75/65ddfa] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[74/a2fb1d] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[c3/e5901b] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

Check failure on line 1 in skip_pseudoalignment = true

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` [friendly_magritte] DSL2 - revision: cb7820872d
[21/4a7ec9] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[3c/61d2a1] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[8d/6349da] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7a/f7d9fc] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[eb/b837a4] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

View more details on GitHub Actions