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Important! Template update for nf-core/tools v3.0.1 #3037

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Important! Template update for nf-core/tools v3.0.1

Important! Template update for nf-core/tools v3.0.1 #3037

GitHub Actions / JUnit Test Report failed Oct 10, 2024 in 0s

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

Annotations

Check failure on line 1 in Test pipeline with default settings

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline with default settings.Params: default 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.09.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [infallible_yonath] 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/7fb7867d706858f1a72d18e1d3ad7c75/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

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                     : infallible_yonath
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/7fb7867d706858f1a72d18e1d3ad7c75
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/7fb7867d706858f1a72d18e1d3ad7c75/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
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[d7/62df10] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[17/3cbdb2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[a2/9228f4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[1f/084eff] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[ec/86b96c] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[37/a38ea3] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[5b/41568e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[d4/935d12] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[01/a782dc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[58/32bbf8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[07/73d46c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[f6/77d33c] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[f9/4e40c2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[e6/a12d61] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[a1/f57d52] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[26/a567a1] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[87/b908ce] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[09/706e90] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[f5/efd2bf] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE (genome_gfp.fasta)
[0c/cf4272] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[dc/f813ff] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[01/f2c030] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[91/d119ed] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
[c0/f270ff] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[49/8aed5e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[4e/bf349c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[63/b619f3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[ec/c42bb5] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_IAA_30M_REP1)
[60/aa08c4] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[c2/116159] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP2)
[8c/b1df7d] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP1)
[cc/70a973] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[21/b5d2ce] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[5d/d0b1f8] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (RAP1_UNINDUCED_REP2)
[8c/52d3fc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[88/279b02] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[48/be8b05] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_IAA_30M_REP1)
[d9/9ed038] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[9f/d79194] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[eb/84a37a] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[17/0cf384] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP2)
[b4/9de86c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[1b/097e3d] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[8f/b66453] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_IAA_30M_REP1)
[c1/f6eff0] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[c5/d3cee2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[7f/4ffc9f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[7b/3e3d00] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP1)
[c7/8d4b64] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[a1/cacbe9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP2)
[b2/ed0937] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[5d/617ece] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN (WT_REP1)
[93/684fe0] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[d5/e3f430] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (RAP1_UNINDUCED_REP2)
[60/ee85b9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[39/b94fe9] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
[60/671c21] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[b1/dbdb14] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[b6/6c520d] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[e7/f68f96] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[1f/fca4da] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[41/4698f0] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
[fc/e4d46a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[c1/b29245] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[93/14a991] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[62/509996] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[cf/1e12d1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[fb/1898a0] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[36/a05133] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[56/78f0ab] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[6f/ee065a] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[1c/1d99c1] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[2a/7a92cf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP2)
[bd/d313e7] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[61/63a17c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[5e/9de64d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[07/dad4fc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[14/6d6e01] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[4c/69c589] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[d0/13ba7b] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[7e/43879d] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[33/e0133c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[33/d9ee9f] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[3e/e2fc12] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[68/dc3cba] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[99/668190] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[dd/056780] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[21/74a0bd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[72/4659bc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[ba/4cc41f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[d5/03db51] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[fa/e710aa] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[fb/ac303b] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[fd/8a8be7] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[89/327701] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[44/d8a88a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[76/ee2330] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[5c/d35df4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[48/e2cc2d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[3d/df3a56] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[66/1746a3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[89/024bd4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[45/2555ab] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[17/1d2abb] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[bd/a502ce] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[26/8c5692] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[f1/0f7b58] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[26/5fcc00] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[51/e150d1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[ee/946ce1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[c8/a4aed4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[04/ea1487] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[8e/c42e95] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[b1/6a3986] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[f6/643ef2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[fa/29dca5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[30/aca971] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[31/41d955] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[6e/483bbd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[e5/58c91d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[46/e3a6b0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[88/09fefb] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[fb/cea16e] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[9b/df4123] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[b8/e98d46] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[d4/2eec4f] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT (WT_REP1)
[28/baffff] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[32/3f5f71] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[f0/4ea608] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[fe/2f475f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[90/67ec6f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[38/e3fc36] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[9a/5734e9] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[e4/1d22d6] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[a2/c51925] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[62/cb9d71] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
[90/82daff] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[8b/f46814] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[9f/e03eda] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[bc/5a1778] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[38/e23309] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES (WT_REP1)
[db/ab7138] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE (null)
[c9/17b3d8] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[e4/4d821f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[9a/2b3f3b] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[5f/68f479] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[f4/07c2a5] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[0a/05974f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[79/9c8518] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[3b/a1f6c1] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[08/111619] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[0c/a4ad6c] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[1e/38319f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[3e/d9a33f] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[a9/189b41] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[99/80e193] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[09/dfa96c] Submitted process > NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[ec/a6a18b] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT
[ae/204290] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[7f/796be5] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[8f/fafed5] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[50/43a3a7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX (WT_REP1)
[5d/950014] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[84/110b45] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[8b/eef0b7] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[41/9959b0] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON
[dd/d96f42] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE (all_samples)
[16/92da9b] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT (all_samples)
[30/e8cf87] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED (all_samples)
[ab/c5a8ea] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED (all_samples)
[8c/4b48bb] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[b7/525119] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[ba/df5c78] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[f2/87bb27] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[bf/0d5b5d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[4e/366048] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[7f/a4f705] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[44/e22e09] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[67/a583aa] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[1f/77ec8b] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[ad/f8d492] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[12/cd0539] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[78/867150] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[1d/8f84f0] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[0b/3eee0d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[e1/f5a2b6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[65/082671] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[e0/edaee5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[d0/c987c6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[54/bf4a63] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[50/55d931] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[06/8d32bf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[0c/64a68b] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP1)
[31/330e41] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[ed/6656d9] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
[d9/4f402a] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
[c7/6faa0f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[72/e555e7] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
-[nf-core/rnaseq] Pipeline completed successfully -
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