Skip to content
nf-core template version comment

Important! Template update for nf-core/tools v3.2.0 #271

Sign in to view logs

Important! Template update for nf-core/tools v3.2.0

Important! Template update for nf-core/tools v3.2.0 #271

GitHub Actions / JUnit Test Report failed Jan 30, 2025 in 0s

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

Annotations

Check failure on line 1 in Test pipeline with dummy UMI settings

See this annotation in the file changed.

@github-actions github-actions / JUnit Test Report

Test pipeline with dummy UMI settings.Params: --aligner hisat2 --umi_dedup_tool 'umicollapse' 

Assertion failed: 

1 of 2 assertions failed
Raw output 
Nextflow stdout:

N E X T F L O W  ~  version 24.12.0-edge
Launching `/home/runner/work/rnaseq/rnaseq/tests/../main.nf` [soggy_perlman] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]

------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/rnaseq 3.19.0dev
------------------------------------------------------
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/f49e8b94b0809135bf4a29582123097b/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
  with_umi                    : true
  umi_dedup_tool              : umicollapse
  umitools_extract_method     : regex
  umitools_bc_pattern         : ^(?P<umi_1>CGA.{8}){s<=2}.*
  umitools_dedup_stats        : true

Alignment options
  aligner                     : hisat2
  pseudo_aligner              : salmon

Optional outputs
  save_umi_intermeds          : true

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/
  trace_report_suffix         : 2025-01-30_14-26-28

Core Nextflow options
  runName                     : soggy_perlman
  containerEngine             : docker
  launchDir                   : /home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b
  workDir                     : /home/runner/work/rnaseq/rnaseq/~/tests/f49e8b94b0809135bf4a29582123097b/work
  projectDir                  : /home/runner/work/rnaseq/rnaseq
  userName                    : runner
  profile                     : test,docker
  configFiles                 : /home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/tests/nextflow.config

!! 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: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  When using '--additional_fasta <FASTA_FILE>' the aligner index will not
  be re-built with the transgenes incorporated by default since you have 
  already provided an index via '--hisat2_index <INDEX>'.

  Set '--additional_fasta <FASTA_FILE> --hisat2_index false --gene_bed false --save_reference'
  to re-build the index with transgenes included and the index and gene BED file will be saved in
  'results/genome/index/hisat2/' for re-use with '--hisat2_index'.

  Ignore this warning if you know that the index already contains transgenes.

  Please see:
  https://github.com/nf-core/rnaseq/issues/556
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[2c/52eab1] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_HISAT2_INDEX (hisat2.tar.gz)
[5a/11c9ef] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[93/b1f40b] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[66/9a119b] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[71/211d31] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[46/8a7200] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (RAP1_UNINDUCED_REP1)
[25/428fe7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP1)
[cc/436ee5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (WT_REP2)
[11/953da5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP2)
[a7/31ab1d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[6b/d712a2] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[f3/cddc19] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (RAP1_IAA_30M_REP1)
[7c/2dd103] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_IAA_30M_REP1)
[5d/17b4dc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[70/10a602] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[ac/f622b6] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[1c/99fa14] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[d3/e8a0cc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[c6/0bc980] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[ea/00ddee] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[93/2eb18f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (WT_REP1)
[eb/46b751] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (WT_REP1)
[fa/fa3231] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC (RAP1_UNINDUCED_REP2)
[d6/fa1590] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:UMITOOLS_EXTRACT (RAP1_UNINDUCED_REP2)
[b5/df4d50] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[c9/65c341] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[e3/118b4a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP1)
[d3/3bff12] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP2)
[15/057f05] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_IAA_30M_REP1)
[44/115719] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[73/643e0d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[38/4f4d0f] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[a0/850342] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[41/6e5652] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP1)
[15/a8e0a2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP2)
[02/253978] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_IAA_30M_REP1)
[f7/99a068] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:HISAT2_EXTRACTSPLICESITES (genome_gfp.gtf)
[f5/6b8f2b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP2)
[81/85a85b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP1)
[9d/8ae9c2] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (RAP1_UNINDUCED_REP2)
[fb/885591] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[95/7bf557] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (RAP1_UNINDUCED_REP2)
[1a/b58f06] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (RAP1_IAA_30M_REP1)
[b4/5135b3] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (WT_REP2)
[93/dcf7b8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (RAP1_UNINDUCED_REP1)
[c9/effacc] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[b5/b1902b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP2)
[29/353174] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_IAA_30M_REP1)
[f4/6924b4] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (RAP1_UNINDUCED_REP1)
[56/69a37b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP2)
[48/44dc08] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[98/f2d8f3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT (WT_REP1)
[22/52c5ec] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:HISAT2_ALIGN (WT_REP1)
[00/a17431] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[2c/411d7f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[da/e073ba] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP2)
[d3/6ae10e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE (RAP1_UNINDUCED_REP2)
[4f/a8c8da] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[a6/88016d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE (RAP1_IAA_30M_REP1)
[b5/a29858] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE (RAP1_UNINDUCED_REP1)
[15/16e3ad] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE (WT_REP2)
[43/bcf99c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT (WT_REP1)
[fd/161259] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[50/d486c3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP2)
[e9/7c5f56] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP2)
[ca/2cea6f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP2)
[ab/6bf9e0] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP2)
[af/20792d] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP2)
[72/452b08] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP2)
[81/0acc69] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP2)
[25/ba49e3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:SAMTOOLS_INDEX (RAP1_IAA_30M_REP1)
[6b/fef1b0] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_IAA_30M_REP1)
[15/a33a78] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_IAA_30M_REP1)
[cd/bd3b25] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_IAA_30M_REP1)
[b7/680db2] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_IAA_30M_REP1)
[21/b4c1f9] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_IAA_30M_REP1)
[6a/dde167] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_IAA_30M_REP1)
[16/b6238a] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (RAP1_UNINDUCED_REP1)
[fa/c244f1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:SAMTOOLS_INDEX (RAP1_UNINDUCED_REP1)
[5e/d5300b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (RAP1_UNINDUCED_REP1)
[54/4d1d92] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (RAP1_UNINDUCED_REP1)
[da/7cda22] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (RAP1_UNINDUCED_REP1)
[cb/94b5f3] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (RAP1_UNINDUCED_REP1)
[9a/93595d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (RAP1_UNINDUCED_REP1)
[b5/d3ce99] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX (WT_REP1)
[77/d3811f] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP2)
[39/927aa6] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP2)
[3e/156dba] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP2)
[ee/6da81d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:SAMTOOLS_INDEX (WT_REP2)
[17/0433b0] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP2)
[1a/5d09ab] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP2)
[c4/76d3b0] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP2)
[e4/6a417c] Submitted process > NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO
[dd/c2cf3a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[f5/cb3bb4] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[ce/7ad175] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
[bb/ffaee3] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[c9/3cd7cd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP2)
[d9/18acf6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP2)
[02/90deef] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP2)
[95/01503c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP2)
[2e/c08718] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP2)
[06/3d7ee3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP2)
[1f/008f2c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP2)
[a5/d065f2] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[2a/c052a2] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP2)
[1c/a9e9a7] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP2)
[4d/20b9b1] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_IAA_30M_REP1)
[61/7a6f5e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_IAA_30M_REP1)
[84/081330] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_IAA_30M_REP1)
[b3/949883] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_IAA_30M_REP1)
[ba/7fc38e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_IAA_30M_REP1)
[39/054baf] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_IAA_30M_REP1)
[4e/ab1776] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_IAA_30M_REP1)
[4c/e67c41] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[02/5c0797] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_IAA_30M_REP1)
[5d/951e41] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_IAA_30M_REP1)
[c0/476e1f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (RAP1_UNINDUCED_REP1)
[bd/5cd764] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (RAP1_UNINDUCED_REP1)
[9f/18b976] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (RAP1_UNINDUCED_REP1)
[9b/a605b9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (RAP1_UNINDUCED_REP1)
[9d/da38e9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (RAP1_UNINDUCED_REP1)
[be/e617e7] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (RAP1_UNINDUCED_REP1)
[dd/48fe49] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (RAP1_UNINDUCED_REP1)
[1a/7fa68d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[96/d32243] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (RAP1_UNINDUCED_REP1)
[51/5b6aa2] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (RAP1_UNINDUCED_REP1)
[b2/241bac] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:UMICOLLAPSE (WT_REP1)
[69/4cdee0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[9c/46c43c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[88/742d4a] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[1b/021997] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[a3/95cff0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[b2/636bb3] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[ce/3082e1] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[f1/96dbe8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[bc/ea73cb] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[32/93b3c0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[3d/53165d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[94/dfb03f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[09/a17abd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[7b/e4da39] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[07/172047] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_ALIGN_HISAT2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[a2/c99ec0] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP2)
[51/394c5e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP2)
[50/98805f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP2)
[d0/c11f7e] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP2)
[0c/6aeae4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP2)
[d6/c38ab9] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP2)
[d8/906ca6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP2)
[ab/6b0925] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP2)
[fb/b978e8] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP2)
[7c/4a7105] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP2)
[00/ad124c] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[de/736a05] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP2)
[41/567997] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[36/59142d] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_IAA_30M_REP1)
[34/2806fb] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[55/3bafb7] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (RAP1_UNINDUCED_REP1)
[3e/c4fab6] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:SAMTOOLS_INDEX (WT_REP1)
[c7/60f6d3] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV (WT_REP1)
[41/6efa1a] Submitted process > NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ (WT_REP1)
[e5/7fdf36] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW (WT_REP1)
[4f/c038e5] Submitted process > NFCORE_RNASEQ:RNASEQ:DUPRADAR (WT_REP1)
[41/9607fd] Submitted process > NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE (WT_REP1)
[19/5bff0f] Submitted process > NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS (WT_REP1)
[f5/6c931b] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[95/2dd3cb] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP2)
[6e/c12d65] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION (WT_REP1)
[28/0067b2] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION (WT_REP1)
[04/78449c] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE (WT_REP1)
[21/16f3ad] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP2)
[a8/52cec5] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION (WT_REP1)
[f6/d75ebe] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT (WT_REP1)
[74/21e071] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_IAA_30M_REP1)
[f5/942d10] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT (WT_REP1)
[9b/cedae4] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION (WT_REP1)
[ac/4b035d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP1)
[11/388fbe] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP2)
[e5/b9858f] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_UNINDUCED_REP1)
[ca/37dccc] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP2)
[3e/13e0bd] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (RAP1_IAA_30M_REP1)
[01/afec06] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP2)
[5f/aae139] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP1)
[01/4b515d] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_IAA_30M_REP1)
[4b/af8736] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (RAP1_UNINDUCED_REP2)
[94/8c46d3] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (RAP1_UNINDUCED_REP1)
[3f/f48036] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT (WT_REP2)
[df/bd52ec] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS (WT_REP1)
[16/0cfc45] Submitted process > NFCORE_RNASEQ:RNASEQ:BAM_DEDUP_UMI_HISAT2:BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE_GENOME:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS (WT_REP1)
[c6/ce061a] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP (WT_REP1)
[5f/ac91c0] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP (WT_REP1)
[fc/231fc1] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE (WT_REP1)
[43/9576c5] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
[91/046817] Submitted process > NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG (WT_REP1)
WARN: Access to undefined parameter `enable_multiqc_ai` -- Initialise it to a default value eg. `params.enable_multiqc_ai = some_value`
[ed/af650d] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-[nf-core/rnaseq] Pipeline completed successfully -
Nextflow stderr:
View more details on GitHub Actions