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Add profile for ARM compatibility #77

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Add profile for ARM compatibility

Add profile for ARM compatibility #77

GitHub Actions / JUnit Test Report failed Oct 23, 2024 in 0s

2 tests run, 0 passed, 0 skipped, 2 failed.

Annotations

Check failure on line 1 in Test pipeline with ribosomal RNA removal

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [trusting_carson] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.17.0dev
------------------------------------------------------
Input/output options
  input                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv
  outdir                      : /home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b/output

Reference genome options
  fasta                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta
  gtf                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz
  gff                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz
  transcript_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta
  additional_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz
  hisat2_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz
  rsem_index                  : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz
  salmon_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz
  hisat2_build_memory         : 3.GB

Read filtering options
  bbsplit_fasta_list          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt
  remove_ribo_rna             : true

UMI options
  umitools_bc_pattern         : NNNN

Alignment options
  pseudo_aligner              : salmon
  min_mapped_reads            : 5

Process skipping options
  skip_bbsplit                : false

Institutional config options
  config_profile_name         : Test profile
  config_profile_description  : Minimal test dataset to check pipeline function

Generic options
  pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/

Core Nextflow options
  runName                     : trusting_carson
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/24a1e6e4fae5e89ee40055637c1d558b/work
  projectDir                  : /home/runner/work/rnaseq/rnaseq
  userName                    : runner
  profile                     : test,docker
  configFiles                 : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.5281/zenodo.1400710

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

* Software dependencies
    https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md

WARN: The following invalid input values have been detected:

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


WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.

  Please see:
  https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[3f/0dadd5] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[5c/22d8bb] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[6d/f0cbce] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[5f/747ddf] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[77/00c442] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[2d/e12492] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[66/a95049] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[1a/70f047] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[2b/45326e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[c6/2e9f6c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[7d/3aa03e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[3d/6ec80e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX ([])
[02/f972f3] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:SORTMERNA_INDEX ([])
[63/357475] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[6b/120e80] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[af/eb02a8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[b7/b00951] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[a9/c3c3e3] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[ad/9c6533] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[c9/8057f0] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[1a/865346] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7f/384b18] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta)
[05/fea5c4] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[83/a2685a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
[ef/d61102] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[28/e4689e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[61/601bec] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[9d/b2a0de] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[09/84267a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (WT_REP2)
[56/8a9291] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (RAP1_IAA_30M_REP1)
[b4/1c5eb9] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (RAP1_UNINDUCED_REP1)
[32/98b687] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (RAP1_UNINDUCED_REP2)
[31/4a10d6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[eb/367f42] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP2)
[fd/5c1d8c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (WT_REP1)
[e4/7cf3ae] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[5c/7df1da] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP1)
[0c/45687a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[38/26f0bf] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)
[d9/787728] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[0c/4e39d8] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)
[ac/c72560] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[e8/5ea402] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[be/5f0ae8] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP2)
[78/f01335] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[e7/45789a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[0b/4b8a61] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[16/383eb3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[52/a5a771] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[e2/abb3c2] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[22/c80fe3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[a9/0c86d8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[e9/062588] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[df/cccaf4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[59/5fd18f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[2b/65108e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)
[06/2d638c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[a2/981914] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[86/f2bcba] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_IAA_30M_REP1)
[83/8a4090] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[e7/9e99ff] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[0c/6823df] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[ce/76ef64] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[7f/e77bed] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[7f/67bc51] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[c7/d87f58] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[26/bbcdbd] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[14/386a5e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[6b/5c44bb] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[5c/c3f662] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[0e/dcaa03] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
[63/217852] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[45/7f3361] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[39/2af3f0] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[ef/5a8ef7] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[9f/0dfc24] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[c4/4bcc79] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[9f/7357de] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[67/35f1b1] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[8a/8268d3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[da/2e021a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[d8/853ef8] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[08/48e5e4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[f1/4ccb69] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[fb/112745] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[c8/05cfec] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[6c/1f322d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[28/7d5502] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[1d/4273c1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[04/c0ac4f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[76/3607a7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[cf/19568e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[fc/a544d8] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[a2/6d98df] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[79/1b51c1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[b6/7a9a55] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[23/3d21d2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[b5/0295a4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[a2/c7f883] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[41/d65270] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[dd/29ec5c] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[ee/3ddbda] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[59/d7f768] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[0f/8dc795] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[b9/43059a] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[f1/35de57] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[8b/fd0ff7] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[9a/f14988] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP1)
[f0/9bb9e4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[3f/7d11a2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[61/ec7508] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[4e/61a1ce] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[37/241f50] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[ec/227caa] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[6b/bc7615] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[31/2139f3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[bc/474e9a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[bc/9fec55] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[d8/934b91] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[16/ad5245] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[15/a70ad0] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
[cb/5399d6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[49/09b180] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[e5/063fa2] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[09/b6daee] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[f2/d8e2a2] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[9d/13220f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[24/58b8b9] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[c4/50ca8a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[bd/c7237d] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[d6/be7d13] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[81/8ef1c3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null)
[14/081174] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[fd/0ff4eb] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[bc/d9eea6] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[d2/5a6fcc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[43/396c36] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[04/5fb90e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[35/35f83f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[9e/f510cc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[69/213e49] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[61/c99c63] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[bb/6a0426] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[ad/a7355e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[08/ab3606] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[44/3d0cc6] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[ec/fdffe2] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[a6/30e443] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[85/039b00] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[22/fcdc8b] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[92/ecf387] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[4e/49d21d] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[b8/b4c111] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[cf/6f3518] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[28/b0a8e6] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[5b/cf5e4a] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[46/e63798] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[84/c824df] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[53/9f6175] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[4f/87a235] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[7e/48f4f8] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[f5/b8080e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[ef/3001f4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
[ca/2fa5ac] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[5c/588ac7] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
[65/d83c3a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[c7/32e2d0] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[17/cbc8a9] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[c5/7af3da] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
[26/b1dad8] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[b3/388ef8] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[87/b24b94] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[79/c8f760] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
[75/671665] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[01/272276] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[49/02e279] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[12/e99c71] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[97/e0568a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[d9/1376f9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[eb/65b85d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[de/100d0c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[ad/d41c50] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[8d/3583ed] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[06/bc13df] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[88/d307ce] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[88/98ff6b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[5f/de257f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[86/0f5037] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[42/9e1e2b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[c3/93d097] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[59/9de2e2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[10/40957b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[19/557e8a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[c2/81bddd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[c4/fc365e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[3a/732370] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[dd/ed0092] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP1)
[39/898778] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
[81/4bac19] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples)
[47/1caf59] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples)
[cf/1b3955] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples)
[36/6800cb] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples)
[51/b2d7cf] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[3d/bc53d4] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[1c/a5db58] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-[nf-core/rnaseq] Pipeline completed successfully -
Nextflow stderr:

Nextflow 24.04.4 is available - Please consider updating your version to it

Check failure on line 1 in Test pipeline with ribosomal RNA removal

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline with ribosomal RNA removal.Params: --remove_ribo_rna - stub 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.04.2
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [nasty_descartes] DSL2 - revision: 85c9b75b8b

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.17.0dev
------------------------------------------------------
Input/output options
  input                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv
  outdir                      : /home/runner/work/rnaseq/rnaseq/~/tests/9850e8cd6173f7f9513c08fb3f75026d/output

Reference genome options
  fasta                       : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genome.fasta
  gtf                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes_with_empty_tid.gtf.gz
  gff                         : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz
  transcript_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta
  additional_fasta            : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz
  hisat2_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz
  rsem_index                  : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/rsem.tar.gz
  salmon_index                : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz
  hisat2_build_memory         : 3.GB

Read filtering options
  bbsplit_fasta_list          : https://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt
  remove_ribo_rna             : true

UMI options
  umitools_bc_pattern         : NNNN

Alignment options
  pseudo_aligner              : salmon
  min_mapped_reads            : 5

Process skipping options
  skip_bbsplit                : false

Institutional config options
  config_profile_name         : Test profile
  config_profile_description  : Minimal test dataset to check pipeline function

Generic options
  pipelines_testdata_base_path: s3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/

Core Nextflow options
  runName                     : nasty_descartes
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/9850e8cd6173f7f9513c08fb3f75026d
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/9850e8cd6173f7f9513c08fb3f75026d/work
  projectDir                  : /home/runner/work/rnaseq/rnaseq
  userName                    : runner
  profile                     : test,docker
  configFiles                 : 

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
* The pipeline
    https://doi.org/10.5281/zenodo.1400710

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

* Software dependencies
    https://github.com/nf-core/rnaseq/blob/master/CITATIONS.md

WARN: The following invalid input values have been detected:

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


WARN: nf-core pipelines do not accept positional arguments. The positional argument `true` has been detected.
HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.

WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Both '--gtf' and '--gff' parameters have been provided.
  Using GTF file as priority.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  '--transcript_fasta' parameter has been provided.
  Make sure transcript names in this file match those in the GFF/GTF file.

  Please see:
  https://github.com/nf-core/rnaseq/issues/753
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[6e/905080] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[43/7e6f40] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[fe/c9c857] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[c9/0fb7df] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[5e/ddc293] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[78/2ac554] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[77/2f008a] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[b2/82e62a] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[b3/abeca4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[19/fb2fd7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[f6/bb2f5a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[5c/a9c8ec] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX ([])
[7c/a27e0b] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:SORTMERNA_INDEX ([])
[9a/6de2f8] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[59/585228] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[97/2df719] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[f2/2d003c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[ab/8158a7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[d2/50e764] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
WARN: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Biotype attribute 'gene_biotype' not found in the last column of the GTF file!

  Biotype QC will be skipped to circumvent the issue below:
  https://github.com/nf-core/rnaseq/issues/460

  Amend '--featurecounts_group_type' to change this behaviour.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[08/2fd9d7] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_transcriptome.fasta)
[0b/d7349d] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_transcriptome.fasta)
[c1/765698] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_transcriptome.gtf)
[63/9856c9] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[17/8c0168] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-[nf-core/rnaseq] Pipeline completed successfully with skipped sampl(es)-
-[nf-core/rnaseq] Please check MultiQC report: 5/5 samples skipped since they failed 10000 trimmed read threshold.-
Nextflow stderr:

Nextflow 24.04.4 is available - Please consider updating your version to it
View more details on GitHub Actions