nf-core linting

Remove existing tests that are duplicated by PUBLISH_GENOME tests #15

Sign in to view logs

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

28 tests run, 10 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` [lethal_easley] DSL2 - revision: 16f4c80bf2
Downloading plugin [email protected]
Downloading plugin [email protected]
[4b/d9fa82] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[4e/8ea5e8] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[c6/345f1c] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[2c/1fcbc4] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[95/096621] 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` [cranky_morse] DSL2 - revision: 4ee6ac0879
[f1/b9855c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[50/ac49ab] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[a6/05a4db] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[92/2dd074] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[34/47e745] 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` [thirsty_khorana] DSL2 - revision: e7f5379587
[0f/e79415] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[98/0eed0f] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[15/b49edd] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[b5/038fdb] 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` [extravagant_bell] DSL2 - revision: 841b65a2c4
[a4/46084b] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[3d/31aa7c] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[7d/8ad6da] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[bb/a049a9] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[f9/36283b] 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` [sleepy_pasteur] DSL2 - revision: cb7820872d
[97/f5fa5b] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[50/b50d80] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[7a/3901a6] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[d4/548712] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[81/3a0655] 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` [nasty_aryabhata] DSL2 - revision: 38988486f6
[a2/dfc967] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[d7/502fd6] Submitted process > PREPARE_GENOME:GFFREAD (genes.gff)
[53/4aa647] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[c0/3c459f] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[d8/5ca523] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[d0/de134f] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[6b/48933b] 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` [nostalgic_ritchie] DSL2 - revision: bd058f72cb
[f8/b0c186] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[8e/a2865e] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[0c/c800f4] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[53/5f1ffa] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[12/c9a36e] 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` [adoring_ardinghelli] DSL2 - revision: 99644d12ee
[ef/0f0ae9] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fasta)
[47/2737e7] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[dc/3a9825] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
[bb/04c4f4] 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_williams] DSL2 - revision: 28200cf32c
[bb/875f42] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[b5/0c7843] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[41/3b6051] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[81/a79faf] Submitted process > PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome_gfp.fasta)
[9d/f27d44] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7e/cb395d] 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` [furious_leavitt] DSL2 - revision: 8e5af7d742
[37/4f279e] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[ad/98dbbd] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[90/7cb397] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[2e/0bfd51] 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` [hungry_meitner] DSL2 - revision: cf5e67199b
[e4/4e1565] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[a7/d06f19] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[6c/cfe99e] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[c1/2dae3a] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ad/c9d1b8] 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` [ecstatic_pasteur] DSL2 - revision: 5630400e88
[11/6c747e] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[74/bc58cc] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[89/734059] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[a8/b145e6] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[50/1c7006] 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` [high_curie] DSL2 - revision: 97a73ef989
[63/f60f47] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[98/e94301] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[da/37cda5] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[92/cc8f84] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ae/07baa4] 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` [suspicious_rutherford] DSL2 - revision: bd6a5cf449
[44/274414] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[5d/ac7819] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[4b/f790b0] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[7c/46e661] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[42/5ffb52] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7f/495f7f] 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` [disturbed_kilby] DSL2 - revision: 3e1d4d30c5
[15/6231a3] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[2d/4b9843] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[4a/061cf6] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[ba/3cc331] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[48/632995] 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` [spontaneous_tesla] DSL2 - revision: e7f5379587
[6e/58b030] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[ac/14a2c0] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[f7/5f7044] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[3a/082214] 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` [cranky_babbage] DSL2 - revision: 841b65a2c4
[e1/256f18] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[96/935578] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[55/f31c2e] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[1b/44e2c7] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[37/d12349] 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` [mad_wozniak] DSL2 - revision: cb7820872d
[89/809a4d] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[2e/488d28] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[8d/cc53ff] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[cc/2e4f30] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[62/4b3cd5] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

View more details on GitHub Actions