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Use BAM_RSEQC subworkflow #587

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Use BAM_RSEQC subworkflow

Use BAM_RSEQC subworkflow #587

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

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@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 23.04.0
Launching `/home/runner/work/nascent/nascent/workflows/tests/aligner/../../../main.nf` [disturbed_majorana] DSL2 - revision: 48ead09e0f
Downloading plugin nf-validation@1.1.3
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        : disturbed_majorana
  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/


[bb/6e4a72] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (cd4_REP2)
[c4/043336] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (jurkat)
[11/1f892f] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (jurkat)
[b1/6a6561] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (cd4_REP2)
[ba/957845] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:GTF2BED (genes_chr21.gtf)
[71/141a3f] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (cd4_REP1)
[7d/96e95d] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (cd4_REP1)
[51/1a2163] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:BOWTIE2_BUILD (GRCh38_chr21.fa)
[e7/498d88] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (GRCh38_chr21.fa)
[86/24ea64] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (cd4_REP2)
[eb/232c3d] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (cd4_REP1)
[73/249719] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BOWTIE2_ALIGN (jurkat)
[d1/4d4b8f] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (cd4_REP2)
[99/0b2570] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (cd4_REP1)
[ba/1d686d] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (cd4_REP2)
[9e/ce41b4] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (cd4_REP1)
WARN: Access to undefined parameter `forwardStranded` -- Initialise it to a default value eg. `params.forwardStranded = some_value`
[64/af0ebc] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (cd4_REP2)
[e3/be8d2c] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (cd4_REP2)
[cb/916a42] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (cd4_REP2)
[d1/dbfe94] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (cd4_REP2)
[11/db97af] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (cd4_REP2)
[bc/e395a9] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (cd4_REP2)
[dd/02b781] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (cd4_REP2)
[22/6eb844] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (cd4_REP2)
[34/52e1fa] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (cd4_REP2)
[59/e86dfe] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (cd4_REP2)
[f1/f00e3d] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (cd4_REP2)
[a3/2e74ab] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (cd4_REP1)
[3d/839aca] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (cd4_REP1)
[b2/e46f27] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (cd4_REP1)
[ed/0e378e] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (cd4_REP1)
[c6/5aae65] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (cd4_REP1)
[c2/22a236] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (cd4_REP1)
[8a/70c727] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (cd4_REP1)
[fe/1bd36f] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (cd4_REP1)
[75/3e76fa] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (cd4_REP1)
[ba/af2c6a] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (cd4_REP1)
[a8/7e30e5] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (jurkat)
[73/21bf3f] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (cd4_REP1)
[96/07da07] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (jurkat)
[eb/27a022] Submitted process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE (cd4)
[ef/2732b7] Submitted process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE (jurkat)
[3e/12515f] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (jurkat)
[3d/eead5a] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (jurkat)
[17/5de3e4] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (jurkat)
[cb/67005a] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (jurkat)
[e8/363f0e] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (jurkat)
[88/ce4455] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (jurkat)
[b0/b19e4e] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (cd4_REP1)
[3e/2a25fa] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (jurkat)
[4d/00c10f] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (jurkat)
[95/8b4f81] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (jurkat)
[c2/0e0e99] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (cd4_REP2)
[28/df0b75] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (jurkat)
[af/2cc52d] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (jurkat)
[2c/0129a9] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (jurkat)
[e7/287798] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (cd4_REP1)
[cc/00038e] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (cd4_REP2)
[f8/9b57cb] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (jurkat)
[4a/d0ca12] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (cd4_REP1)
[1a/dac624] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (cd4_REP2)
[8e/62502f] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKETAGDIRECTORY (jurkat)
[ae/a56305] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKETAGDIRECTORY (cd4)
[2a/93c7f0] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (jurkat)
[c2/dc604c] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKEUCSCFILE (jurkat)
[b8/9b95d6] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_FINDPEAKS (jurkat)
[6b/072a34] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKEUCSCFILE (cd4)
[78/136e0e] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_FINDPEAKS (cd4)
[17/c15507] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_POS2BED (jurkat)
[73/1a3be1] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_POS2BED (cd4)
[25/40a406] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT_FILTER (jurkat)
[e4/e728b9] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT (jurkat)
[cb/8de0cb] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT_FILTER (cd4)
[2d/15640a] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT (cd4)
[9a/930891] Submitted process > NFCORE_NASCENT:NASCENT:MULTIQC
-[nf-core/nascent] Pipeline completed successfully-
Nextflow stderr:
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