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Use BAM_RSEQC subworkflow #589

Use BAM_RSEQC subworkflow

Use BAM_RSEQC subworkflow #589

GitHub Actions / JUnit Test Report failed Aug 5, 2024 in 0s

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

Annotations

Check failure on line 1 in HISAT2

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@github-actions github-actions / JUnit Test Report

HISAT2.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` [nostalgic_bernard] 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        : nostalgic_bernard
  containerEngine: docker
  launchDir      : /home/runner/work/nascent/nascent/~/tests/65f3ac25582da395da93c750c8251c9
  workDir        : /home/runner/work/nascent/nascent/~/tests/65f3ac25582da395da93c750c8251c9/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/65f3ac25582da395da93c750c8251c9/output

Alignment Options
  aligner        : hisat2

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
  hisat2_index   : https://raw.githubusercontent.com/nf-core/test-datasets/nascent/reference/GRCh38_chr21_hisat2.tar.gz

!! 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/


[b1/3797fc] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (jurkat)
[59/c1b453] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (cd4_REP1)
[e5/827103] Submitted process > NFCORE_NASCENT:NASCENT:FASTQC (cd4_REP2)
[2c/8df163] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (cd4_REP2)
[f3/a3915c] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (jurkat)
[4b/3d58e3] Submitted process > NFCORE_NASCENT:NASCENT:FASTP (cd4_REP1)
[35/be65d2] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:GTF2BED (genes_chr21.gtf)
[d6/3acede] Submitted process > NFCORE_NASCENT:NASCENT:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (GRCh38_chr21.fa)
[f5/74a042] Submitted process > NFCORE_NASCENT:NASCENT:UNTAR_HISAT2_INDEX (GRCh38_chr21_hisat2.tar.gz)
WARN: Access to undefined parameter `seq_center` -- Initialise it to a default value eg. `params.seq_center = some_value`
WARN: Access to undefined parameter `save_unaligned` -- Initialise it to a default value eg. `params.save_unaligned = some_value`
[37/57d5c4] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (cd4_REP2)
[be/d109de] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (cd4_REP1)
[02/512c13] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (jurkat)
[9f/e42e4e] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (cd4_REP2)
[ec/ecef5a] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (cd4_REP1)
[2b/333f8e] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (cd4_REP2)
[2c/5ee98b] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2: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`
[05/24bdb8] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (cd4_REP2)
[0c/006c66] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (cd4_REP2)
[de/959b6f] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (cd4_REP2)
[2d/0413b5] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (cd4_REP2)
[69/df5bc8] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (cd4_REP2)
[97/d0a89e] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (cd4_REP2)
[d4/7999db] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (cd4_REP2)
[f3/26d916] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (cd4_REP2)
[6a/57da57] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (cd4_REP2)
[fa/e16a06] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (cd4_REP2)
[7e/abd6f1] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (cd4_REP2)
[2a/395a7a] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (cd4_REP1)
[44/0d5125] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (cd4_REP1)
[d5/dd6326] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (cd4_REP1)
[31/4dde3f] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (cd4_REP1)
[50/944a53] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (cd4_REP1)
[57/746e1a] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (cd4_REP1)
[10/fefc0d] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (cd4_REP1)
[57/d3fa1e] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (cd4_REP1)
[73/3ab14a] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (cd4_REP1)
[86/641a7c] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (cd4_REP1)
[88/0dbe24] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (cd4_REP1)
[63/83976c] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (jurkat)
[87/411530] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (jurkat)
[3a/b6001e] Submitted process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE (cd4)
[1d/c42115] Submitted process > NFCORE_NASCENT:NASCENT:SUBREAD_FEATURECOUNTS_GENE (jurkat)
[cd/59e2d6] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDISTRIBUTION (jurkat)
[fa/2d30f5] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_LCEXTRAP (jurkat)
[29/1cb6d0] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_PLUS (jurkat)
[02/5f4cb9] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DREG_PREP (jurkat)
[80/29218b] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BBMAP_PILEUP (jurkat)
[4e/49d3c4] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:BEDTOOLS_GENOMECOV_MINUS (jurkat)
[c8/9ecec9] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_READDUPLICATION (jurkat)
[11/0bd82c] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:BAM_RSEQC:RSEQC_INFEREXPERIMENT (jurkat)
[0c/93a125] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_MINUS (jurkat)
[e7/6cb435] Submitted process > NFCORE_NASCENT:NASCENT:COVERAGE_GRAPHS:DEEPTOOLS_BAMCOVERAGE_PLUS (jurkat)
[35/4bff27] Submitted process > NFCORE_NASCENT:NASCENT:QUALITY_CONTROL:PRESEQ_CCURVE (jurkat)
[2b/1bf2e4] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (cd4_REP1)
[11/9ae9f8] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (cd4_REP2)
[94/41454b] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (jurkat)
[04/0bc63d] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (jurkat)
[9e/c5e060] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (cd4_REP1)
[6a/0430a2] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (cd4_REP2)
[22/dc0448] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:PINTS_CALLER (cd4)
[44/ea3bfc] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:PINTS_CALLER (jurkat)
[2c/b93a4f] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKETAGDIRECTORY (cd4)
[c4/b2b148] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKETAGDIRECTORY (jurkat)
[71/696651] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (cd4_REP2)
[7a/4e2bc1] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (jurkat)
[1b/eb7295] Submitted process > NFCORE_NASCENT:NASCENT:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (cd4_REP1)
[6d/bfc113] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_FINDPEAKS (cd4)
[40/b21991] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKEUCSCFILE (cd4)
[60/7a6236] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_FINDPEAKS (jurkat)
[b4/e33932] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_MAKEUCSCFILE (jurkat)
[9f/ea241f] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_POS2BED (cd4)
[89/034c77] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:HOMER_GROSEQ:HOMER_POS2BED (jurkat)
[3a/3c664c] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT_FILTER (cd4)
[a9/8dd96c] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT_FILTER (jurkat)
[90/bb6860] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT (cd4)
[f8/53d310] Submitted process > NFCORE_NASCENT:NASCENT:TRANSCRIPT_INDENTIFICATION:BEDTOOLS_INTERSECT (jurkat)
[b8/c259a3] Submitted process > NFCORE_NASCENT:NASCENT:MULTIQC
-[nf-core/nascent] Pipeline completed successfully-
Nextflow stderr: