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Refactor tests #365

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Refactor tests

Refactor tests #365

GitHub Actions / JUnit Test Report failed Aug 4, 2024 in 0s

1 tests run, 0 passed, 0 skipped, 1 failed.

Annotations

Check failure on line 1 in Bowtie2

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Bowtie2.Should run with defaults 

Assertion failed: 

1 of 3 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.04.4
Launching `/home/runner/work/nascent/nascent/workflows/tests/aligner/../../../main.nf` [big_church] DSL2 - revision: 48ead09e0f
Downloading plugin [email protected]
WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/nascent v2.3.0dev
------------------------------------------------------
Core Nextflow options
  runName        : big_church
  containerEngine: docker
  launchDir      : /home/runner/work/nascent/nascent/~/tests/dbca444ee7e85f14f1f56535347eb4b2
  workDir        : /home/runner/work/nascent/nascent/~/tests/dbca444ee7e85f14f1f56535347eb4b2/work
  projectDir     : /home/runner/work/nascent/nascent
  userName       : runner
  profile        : docker
  configFiles    : 

Input/output options
  input          : /home/runner/work/nascent/nascent/assets/small_samplesheet.csv
  outdir         : /home/runner/work/nascent/nascent/~/tests/dbca444ee7e85f14f1f56535347eb4b2/output

Alignment Options
  aligner        : bowtie2

Transcript Identification Options
  assay_type     : GROseq
  skip_grohmm    : true
  tuning_file    : /home/runner/work/nascent/nascent/tests/config/tuningparams_small.csv
  filter_bed     : /home/runner/work/nascent/nascent/tests/config/unwanted_region.bed
  intersect_bed  : /home/runner/work/nascent/nascent/tests/config/wanted_region.bed

Reference genome options
  fasta          : https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21.fa
  gtf            : https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/genes_chr21.gtf

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/nascent for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.7245273

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/nascent/blob/master/CITATIONS.md
------------------------------------------------------
WARN: The following invalid input values have been detected:

* --modules_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/modules/


[69/7df3b0] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (cd4_REP2)
[f4/5a8eb3] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (cd4_REP1)
[ca/32ba5c] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (cd4_REP1)
[d4/5525be] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:GTF2BED (genes_chr21.gtf)
[70/77586c] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (jurkat)
[42/55ee4b] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (cd4_REP2)
[14/b72629] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (jurkat)
[dd/7d1783] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (GRCh38_chr21.fa)
[db/1e1eea] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:BOWTIE2_BUILD (GRCh38_chr21.fa)
[e7/9615cb] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (jurkat)
[9e/11e028] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (cd4_REP1)
[12/969f17] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (cd4_REP2)
[d5/ca8fef] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (jurkat)
[77/0d2189] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (cd4_REP1)
[85/7a0412] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (jurkat)
[cc/b61683] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_READDUPLICATION (jurkat)
[77/96f853] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_INFEREXPERIMENT (jurkat)
[fb/afec08] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_READDISTRIBUTION (jurkat)
[cd/c872b0] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (jurkat)
[6d/7a8057] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (jurkat)
[14/705525] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (jurkat)
WARN: Access to undefined parameter `forwardStranded` -- Initialise it to a default value eg. `params.forwardStranded = some_value`
[67/7e82ed] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (jurkat)
[48/6cf393] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (jurkat)
[01/73f780] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_READDUPLICATION (cd4_REP1)
[f6/5d9229] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (cd4_REP1)
[5b/afb94d] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_INFEREXPERIMENT (cd4_REP1)
[a1/c994aa] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (cd4_REP1)
[99/1583f7] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (cd4_REP1)
[64/f7aa5a] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (cd4_REP1)
[8c/9ac94b] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (cd4_REP1)
[78/91af82] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (cd4_REP1)
[a1/3d0019] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_READDISTRIBUTION (cd4_REP1)
[ac/cd8edd] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (cd4_REP2)
[cb/6de05b] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (jurkat)
[23/9fb143] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (jurkat)
[b5/4aecdb] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (jurkat)
[e8/c21387] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (cd4_REP1)
[56/dd5d94] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (cd4_REP1)
[04/f1f38c] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (cd4_REP1)
[c0/fc0c57] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (cd4_REP2)
[f9/cbbc12] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (cd4_REP2)
[75/44f4d3] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (cd4_REP2)
[ab/9b4374] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (cd4_REP2)
[44/b974c5] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_READDISTRIBUTION (cd4_REP2)
[70/557c44] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_INFEREXPERIMENT (cd4_REP2)
[0f/3d82b3] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (cd4_REP2)
[c9/a2a36f] Submitted process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE (cd4)
[03/ff88c2] Submitted process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE (jurkat)
[fe/ce6875] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (cd4_REP2)
[cd/17a6d8] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:RSEQC_READDUPLICATION (cd4_REP2)
[74/2a39fb] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (cd4_REP2)
[fe/993526] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (cd4_REP2)
[2c/1b00f5] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (jurkat)
[8e/47d9a8] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (cd4_REP2)
[b3/e96424] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (cd4_REP1)
[b0/7e2795] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (jurkat)
[07/01b9a2] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (cd4_REP2)
[21/860aeb] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (cd4_REP1)
[de/84cecf] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (cd4_REP1)
[23/8cba97] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (cd4_REP2)
[4b/283578] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKETAGDIRECTORY (cd4)
[01/19c9ab] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (cd4_REP2)
[96/990ea8] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKETAGDIRECTORY (jurkat)
[cd/a2879f] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (jurkat)
[3e/485d22] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKEUCSCFILE (jurkat)
[49/a0c75e] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_FINDPEAKS (jurkat)
[ff/1e5313] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKEUCSCFILE (cd4)
[a5/424083] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_FINDPEAKS (cd4)
[ef/a40c97] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_POS2BED (jurkat)
[69/b2acd0] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_POS2BED (cd4)
[21/61a274] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT_FILTER (jurkat)
[90/1a2753] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT (jurkat)
[ea/51253d] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT_FILTER (cd4)
[15/ee99e7] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT (cd4)
[29/a56d29] Submitted process > NFCORE_NASCENT:NASCENT:MULTIQC
-[nf-core/nascent] Pipeline completed successfully-
Nextflow stderr:
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