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` [happy_pesquet] DSL2 - revision: 16f4c80bf2
Downloading plugin [email protected]
Downloading plugin [email protected]
[06/f4475c] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[cb/8c9622] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[46/c292f6] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[31/0c9279] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[02/ed631d] 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` [golden_mahavira] DSL2 - revision: 4ee6ac0879
[5c/72f169] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[de/6d248e] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[dc/f51b35] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7d/389a3b] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[f7/b05b73] 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` [ridiculous_raman] DSL2 - revision: e7f5379587
[6d/5f1c69] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[78/90ab5b] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[7c/e18c0d] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[21/fd7c04] 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` [drunk_tuckerman] DSL2 - revision: 841b65a2c4
[f7/6a8b3f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[fa/4103b0] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[fe/155511] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[4b/811025] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[f0/1fdcb7] 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` [festering_sammet] DSL2 - revision: cb7820872d
[ab/17c8b7] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[65/4b4c48] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[46/d2826d] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7f/7f3d30] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[37/18e3ac] 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` [confident_goldberg] DSL2 - revision: 38988486f6
[7e/f3380c] Submitted process > PREPARE_GENOME:GFFREAD (genes.gff)
[8c/2b2414] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[33/32fe87] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[67/b2ff4b] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[97/9275e1] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[24/366321] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[12/1f0dc6] 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` [pensive_curran] DSL2 - revision: bd058f72cb
[f6/99a933] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[f6/d01560] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[66/50349e] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[63/9daad2] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[ca/58934b] 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` [reverent_lattes] DSL2 - revision: 99644d12ee
[3d/81195f] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
[69/3cc26f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[39/51cef3] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome.fasta)
[e8/8a5bb1] 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` [irreverent_wescoff] DSL2 - revision: 28200cf32c
[9f/be547f] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[8f/b5c8fb] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[66/f3b160] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[c2/f3f20a] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[52/53ecb4] Submitted process > PREPARE_GENOME:MAKE_TRANSCRIPTS_FASTA (rsem/genome_gfp.fasta)
[7c/ec55ae] 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` [loving_dubinsky] DSL2 - revision: 8e5af7d742
[ad/16aa31] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[b8/a9c18e] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[6c/cc9a57] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[01/2dd656] 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` [exotic_wilson] DSL2 - revision: cf5e67199b
[62/fd1081] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[3d/a342eb] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[d6/e1490e] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[ae/e8f55f] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[67/1b6813] 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` [nice_snyder] DSL2 - revision: 5630400e88
[64/79ea35] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[20/b90c15] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[a6/cdf729] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[c1/1ae545] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[bb/a8efc6] 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` [silly_galileo] DSL2 - revision: 97a73ef989
[fc/7eba84] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[2c/a88780] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[5c/c37552] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[3d/69a541] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[d0/4321df] 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` [irreverent_booth] DSL2 - revision: bd6a5cf449
[23/01e42d] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[5b/737f10] Submitted process > PREPARE_GENOME:PREPROCESS_TRANSCRIPTS_FASTA_GENCODE (transcriptome.fasta)
[e7/15fd46] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[3a/0a1b7c] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[3c/ff03e8] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[18/1a4e88] 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` [peaceful_northcutt] DSL2 - revision: 3e1d4d30c5
[87/7b0574] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[e9/e0d041] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[a8/e16a26] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[66/5535a7] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[a6/f60e05] 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` [modest_newton] DSL2 - revision: e7f5379587
[84/f766b1] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[18/d63475] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[25/078687] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[c6/7437ae] 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` [deadly_khorana] DSL2 - revision: 841b65a2c4
[7d/040c10] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[79/c11f25] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[49/6353d4] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[97/fcba9b] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[25/2e6dc1] 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` [cheeky_sax] DSL2 - revision: cb7820872d
[76/d38dca] Submitted process > PREPARE_GENOME:GTF_FILTER (genome.fasta)
[c6/5c5f42] Submitted process > PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[c4/187ebe] Submitted process > PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[5d/e8f526] Submitted process > PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[5c/f95a02] Submitted process > PREPARE_GENOME:BBMAP_BBSPLIT (null)
Nextflow stderr:

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