nf-core linting

Remove existing tests that are duplicated by PUBLISH_GENOME tests #15

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

21 tests run, 3 passed, 0 skipped, 18 failed.

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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` [mighty_shockley] DSL2 - revision: 16f4c80bf2
Downloading plugin [email protected]
Downloading plugin [email protected]
[62/d23faf] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[86/8ff369] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[49/2306c8] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[61/8a132b] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[72/d1607c] 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` [lonely_meucci] DSL2 - revision: 4ee6ac0879
[a9/700b7c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[ad/2996ef] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[84/eb7f5c] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[3f/1afe75] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7a/e4c45e] 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` [elegant_kalman] DSL2 - revision: e7f5379587
[fb/3fba5b] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[9a/66598b] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ea/730cc7] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[ba/ee1265] 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` [compassionate_euler] DSL2 - revision: 841b65a2c4
[74/b88663] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[2b/d4b986] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[3e/ad83f3] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[bb/4bad88] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[54/3c5d56] 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` [adoring_lattes] DSL2 - revision: cb7820872d
[fa/f95c99] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[a5/45b586] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[39/69203a] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[b5/c51a0c] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[50/416fdb] 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` [irreverent_meitner] DSL2 - revision: 38988486f6
[65/9ac76c] Submitted process > PREPARE_GENOME:GFFREAD (genes.gff)
[ec/9f4569] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[15/fd4b0a] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[76/8ab48c] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[f8/b21646] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[57/8e98d0] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[0a/030604] 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` [desperate_ampere] DSL2 - revision: bd058f72cb
[71/2a45f3] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[2a/f47b08] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[c0/9d0c51] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[23/835f30] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[68/b2ab2b] 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` [dreamy_bernard] DSL2 - revision: 99644d12ee
[e7/c7ec17] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fasta)
[7b/3eecc1] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[bd/9b2c1a] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
[d3/7537af] 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` [cheesy_laplace] DSL2 - revision: 28200cf32c
[36/9df23a] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[ef/b23a52] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[a9/a58ed0] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[bc/61f49a] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[ac/566a1d] Submitted process > PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome_gfp.fasta)
[56/116766] 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` [hungry_heisenberg] DSL2 - revision: 8e5af7d742
[08/1e8d97] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[92/46d59f] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[cd/df69f6] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[89/895020] 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` [extravagant_lattes] DSL2 - revision: cf5e67199b
[5d/7a7469] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[e8/a63233] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[6b/e6e6b2] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[f4/518c8c] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[27/edf25b] 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` [crazy_wilson] DSL2 - revision: 5630400e88
[78/fd9f6a] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[4a/feb977] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[94/9f8f74] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[01/7052b8] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[06/0e60cc] 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` [elegant_sinoussi] DSL2 - revision: 97a73ef989
[2a/05cede] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[27/a33e3c] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[3e/ad1d6f] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[cd/37e957] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[9a/4970b6] 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` [lethal_linnaeus] DSL2 - revision: bd6a5cf449
[6e/5a8f89] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[68/c11cdd] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[a5/81f252] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[77/2494a9] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[11/244e6b] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[cc/bae99b] 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` [clever_euler] DSL2 - revision: 3e1d4d30c5
[22/d5582c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[2a/7a6477] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[f0/d15d3e] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[02/1351a3] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[51/05cd64] 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` [naughty_edison] DSL2 - revision: e7f5379587
[f3/079f84] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[38/8a01f8] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[49/74ec9e] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[64/bec1f1] 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` [insane_goldberg] DSL2 - revision: 841b65a2c4
[e3/949d86] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[6c/615f14] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[88/008d2b] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[a8/3711e2] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[af/9b577a] 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` [backstabbing_descartes] DSL2 - revision: cb7820872d
[5a/629283] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[11/c6cba9] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[b3/aa8b21] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[78/646526] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[dc/c99cad] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

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