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Bump lots of modules so that conda versions have arm builds #46

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Bump lots of modules so that conda versions have arm builds

Bump lots of modules so that conda versions have arm builds #46

GitHub Actions / JUnit Test Report failed Oct 21, 2024 in 0s

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

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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` [scruffy_swirles] 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                     : scruffy_swirles
  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
[1d/cd5a38] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[bb/7c5b00] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[52/067048] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[cc/adfc6f] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[88/e61a84] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[14/6ce6b8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[be/b42cbd] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[d9/945090] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[dc/d19216] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[3a/83958e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[31/29c2cf] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[66/dc6247] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:SORTMERNA_INDEX ([])
[97/0b7104] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX ([])
[cb/35f57c] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[04/7fd99b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[d1/e7d4a4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[eb/fb6941] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[d4/05fb49] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[7f/4fcbe7] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[11/2e4e8f] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[d3/c21aa0] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[7c/97eead] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta)
[05/72979e] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[bd/7e47c3] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
[df/0f161c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[55/ee48d6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[e6/70b8c6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[ae/7ca175] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[81/3d5e82] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (WT_REP2)
[95/13c2f2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (RAP1_IAA_30M_REP1)
[5b/8a399e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (RAP1_UNINDUCED_REP1)
[68/52b840] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (RAP1_UNINDUCED_REP2)
[d1/ab6190] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA (WT_REP1)
[96/fdbf02] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP2)
[07/52b4ed] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[4f/a48b34] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[42/1fe391] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)
[d6/3f4802] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP1)
[7e/24fd15] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[4d/92db15] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[86/2290a4] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)
[04/6914da] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[aa/7ed7d6] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[80/b849f9] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP2)
[aa/a84755] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[6f/ea606e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[08/d0c682] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[c9/7214d3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[da/6bbe64] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[56/e49cfc] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[22/54c9ee] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[4e/0cbe96] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[7f/0a49b9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[76/8832c1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[09/97b077] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[a9/fa9d78] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[a0/22eb9e] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)
[4a/3c9eea] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[a9/e26bea] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_IAA_30M_REP1)
[01/85d34e] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[09/199fc1] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[95/f35f10] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
[b1/39f38e] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[6a/938eb3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[80/6fe065] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[6d/fd717b] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[de/7f06ad] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[64/523780] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[8c/b20033] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[1c/a31cc5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[eb/fe05f3] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[b9/d30239] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[7e/81dae1] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[66/63aa42] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[7d/3ee25a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[a5/74f967] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[c6/3add93] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[17/8f2757] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[b4/96f93c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[a9/cce448] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[75/89edc9] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[c9/9aa265] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[53/fb3903] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[9f/35fd35] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[a7/0adceb] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[69/b9a75d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[2c/e1e480] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[b5/c27940] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[6d/7eee37] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[d7/5eb825] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[70/76928d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[88/6934a0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[84/efe5c7] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[ed/4a2b02] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[f9/594fe2] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[87/b3644a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[24/bf6111] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[ad/66f4f5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[ff/727fd0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[ad/e6e7a7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[8c/1260ba] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[a6/408a04] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[2b/8bba1f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[cc/fa99f8] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[29/723e15] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[42/64af34] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[fd/c6a9bc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[d3/fe82fe] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[06/2d11c7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[3e/04d804] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[2a/f99e1c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[8c/3a5660] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[c0/0f1e1d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[a8/195749] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[4f/365ae6] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[0c/727846] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP1)
[ef/553d86] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[46/0190f2] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[81/8ea194] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[68/47875c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[78/70b36d] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
[01/50a7d6] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[fb/9c6a3a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[30/163700] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[66/435282] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[3e/d71358] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[74/8c2528] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[79/92390d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[04/32f999] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[df/3d0fbe] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[b1/2ee179] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[2f/981b4c] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null)
[09/cab3da] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[7c/e3bf69] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[f4/a0c8ab] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[bb/e11c0b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[35/06ba5a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[40/562fed] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[9d/acad2a] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[bf/5271d0] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[f0/3585a8] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[81/0df1b8] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[1e/c78125] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[5b/e17f47] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
[80/6681ae] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[c2/258b45] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[97/abb002] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[22/47097a] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[a5/90d078] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[b7/7e7b80] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[9d/fc559d] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[d5/4a5802] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[83/a93018] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[1a/41f445] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[db/d117e8] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[d6/bea6fa] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[ff/9b5c38] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[b4/35652f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[e1/90aea6] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[f8/f58b20] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[04/f11b73] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[73/c225e4] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[ae/8e4fc3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
[fd/657823] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[61/44ba30] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[f0/ff04ce] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[56/2ed4f6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
[97/94b53d] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[a4/313643] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[3e/22be29] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[a4/ca02b5] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[55/3470f7] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[94/e5cd8d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
[a5/b6dff2] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
[c0/73cbdc] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples)
[46/2f6785] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples)
[36/6aea7f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples)
[50/95c4a5] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples)
[ff/f867a6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[49/a68c69] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[f4/ce47e0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[3f/f8a56f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[17/291d08] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[07/74dc90] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[02/306bb8] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[45/f28e84] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[f9/9313a4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[16/258f4f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[bd/331a6d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[9f/0b8991] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[08/35910c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[8c/6f6e24] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[0c/25eb88] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[83/70aeda] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[52/e01c3d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[78/affd27] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[08/408c40] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[4b/bc54af] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[5f/30949c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[1a/2f0ccc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[4c/a70765] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP1)
[b8/b70b36] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[8b/fee62b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[3b/f3035b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[ea/cd4c47] 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` [zen_goldberg] 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                     : zen_goldberg
  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
[03/69f3ad] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[4b/1da7ad] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[82/cbdc19] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[1e/42e2ab] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[48/8e6bbd] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[e0/9e9f6b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[4a/621cbb] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[59/7b520c] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[f1/d126dd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[68/39e725] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[64/4e04e2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[ed/e598b3] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:SORTMERNA_INDEX ([])
[06/54872e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:SORTMERNA_INDEX ([])
[86/b71e4d] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[76/c5e0e8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[cf/f5dd63] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[12/ed315b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[63/7ebb69] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[00/1589f3] 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.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[94/651ee1] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_transcriptome.gtf)
[03/3656bf] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_transcriptome.fasta)
[a2/c109b9] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_transcriptome.fasta)
[3e/f8ed02] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[ec/948380] 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