ARM Megatests #336
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Apr 11, 2025 in 0s
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Check failure on line 1 in Test pipeline with Kallisto, skipping both QC and alignment
github-actions / JUnit Test Report
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment
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` [special_leibniz] DSL2 - revision: 85c9b75b8b
Downloading plugin [email protected]
WARN: Invalid config manifest attribute `contributors`
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[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/rnaseq 3.19.0dev[0m
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[0;34mcontainer.UMITOOLS_EXTRACT : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UMITOOLS_PREPAREFORRSEM : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UNTAR : [0;32mcommunity.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc[0m
[0;34mlaunchDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/3bdf2943960b42549e1eb2f05f2109d[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/3bdf2943960b42549e1eb2f05f2109d/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/rnaseq/rnaseq[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m/home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/tests/nextflow.config[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* 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: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--skip_alignment' parameter has been provided.
Skipping alignment, genome-based quantification and all downstream QC processes.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[40/18844c] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[be/18e5fa] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[36/9f7905] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:KALLISTO_INDEX (transcriptome.fasta)
[cb/b19549] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[98/00f99b] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[76/d68b10] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[5e/03c106] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[17/564bab] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[d6/3d2440] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[64/ac6f97] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[68/058975] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[4f/eaafc6] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[f7/d07f5d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[3f/e1af1e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[03/416c6d] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[d1/515136] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[62/7190fb] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[48/2724d1] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP1)
[e8/c3db3e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[07/e7067e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_IAA_30M_REP1)
[a6/2490a8] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP2)
[7f/de35fb] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (RAP1_UNINDUCED_REP2)
[ea/a837f9] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_gfp.fasta)
[88/1202fc] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_gfp.gtf)
[f4/f314e2] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
[f6/8c1835] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_TRIMMING (WT_REP1)
[bc/a47045] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_IAA_30M_REP1)
[70/e4b6b0] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP1)
[b8/7fd748] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (RAP1_UNINDUCED_REP2)
[74/83716f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP2)
[03/f5bd5c] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT (WT_REP1)
[cc/ddf3d7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP1)
[54/5b1107] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_IAA_30M_REP1)
[63/64b2cb] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (RAP1_UNINDUCED_REP2)
[7b/8d05af] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP2)
[7f/d4e82b] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT (RAP1_UNINDUCED_REP1)
[e5/73b7d1] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT (RAP1_IAA_30M_REP1)
[a2/f60f30] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT (RAP1_UNINDUCED_REP2)
[9c/6e6479] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT (WT_REP2)
[e8/af952f] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT_AFTER_BBSPLIT (WT_REP1)
[b1/26757e] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE (WT_REP1)
[b4/90c82b] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT (WT_REP1)
[9f/3a7a1e] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:KALLISTO_QUANT (WT_REP1)
[61/98a8e8] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE (null)
[e5/0f7405] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT
[94/9b0491] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT (all_samples)
[7e/034f69] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE (all_samples)
[6a/927233] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED (all_samples)
[23/29d8a4] Submitted process > NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED (all_samples)
WARN: Access to undefined parameter `enable_multiqc_ai` -- Initialise it to a default value eg. `params.enable_multiqc_ai = some_value`
[67/a0224b] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-[0;35m[nf-core/rnaseq][0;32m Pipeline completed successfully [0m-
Nextflow stderr:
Nextflow 24.10.5 is available - Please consider updating your version to it
Check failure on line 1 in Test pipeline with Kallisto, skipping both QC and alignment
github-actions / JUnit Test Report
Test pipeline with Kallisto, skipping both QC and alignment.Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - 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` [small_mccarthy] DSL2 - revision: 85c9b75b8b
WARN: Invalid config manifest attribute `contributors`
-[2m----------------------------------------------------[0m-
[0;32m,--.[0;30m/[0;32m,-.[0m
[0;34m ___ __ __ __ ___ [0;32m/,-._.--~'[0m
[0;34m |\ | |__ __ / ` / \ |__) |__ [0;33m} {[0m
[0;34m | \| | \__, \__/ | \ |___ [0;32m\`-._,-`-,[0m
[0;32m`._,._,'[0m
[0;35m nf-core/rnaseq 3.19.0dev[0m
-[2m----------------------------------------------------[0m-
[1mInput/output options[0m
[0;34minput : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/samplesheet/v3.10/samplesheet_test.csv[0m
[0;34moutdir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/54655b7600b646af862a2f183d5309ad/output[0m
[1mReference genome options[0m
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[0;34mgff : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/genes.gff.gz[0m
[0;34mtranscript_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/transcriptome.fasta[0m
[0;34madditional_fasta : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/gfp.fa.gz[0m
[0;34mhisat2_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/hisat2.tar.gz[0m
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[0;34msalmon_index : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/salmon.tar.gz[0m
[0;34mhisat2_build_memory : [0;32m3.GB[0m
[1mRead filtering options[0m
[0;34mbbsplit_fasta_list : [0;32mhttps://raw.githubusercontent.com/nf-core/test-datasets/626c8fab639062eade4b10747e919341cbf9b41a/reference/bbsplit_fasta_list.txt[0m
[1mUMI options[0m
[0;34mumitools_bc_pattern : [0;32mNNNN[0m
[1mAlignment options[0m
[0;34mpseudo_aligner : [0;32mkallisto[0m
[1mProcess skipping options[0m
[0;34mskip_bbsplit : [0;32mfalse[0m
[0;34mskip_alignment : [0;32mtrue[0m
[0;34mskip_qc : [0;32mtrue[0m
[1mInstitutional config options[0m
[0;34mconfig_profile_name : [0;32mTest profile[0m
[0;34mconfig_profile_description : [0;32mMinimal test dataset to check pipeline function[0m
[1mGeneric options[0m
[0;34mpipelines_testdata_base_path : [0;32ms3://ngi-igenomes/testdata/nf-core/pipelines/rnaseq/3.15/[0m
[0;34mtrace_report_suffix : [0;32m2025-04-11_19-57-16[0m
[1mCore Nextflow options[0m
[0;34mrunName : [0;32msmall_mccarthy[0m
[0;34mcontainerEngine : [0;32mdocker[0m
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[0;34mcontainer.BRACKEN_BRACKEN : [0;32mcommunity.wave.seqera.io/library/bracken:2.9--3d5af74ed6966fc1[0m
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[0;34mcontainer.DESEQ2_QC : [0;32mcommunity.wave.seqera.io/library/r-base_r-optparse_r-ggplot2_r-rcolorbrewer_pruned:d06fadc02f8422a2[0m
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[0;34mcontainer.FASTQC : [0;32mcommunity.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29[0m
[0;34mcontainer.FQ_LINT : [0;32mcommunity.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa[0m
[0;34mcontainer.FQ_SUBSAMPLE : [0;32mcommunity.wave.seqera.io/library/fq:0.12.0--45ea0ea1c4d20daa[0m
[0;34mcontainer.GFFREAD : [0;32mcommunity.wave.seqera.io/library/gffread:0.12.7--33b95f1cfcc0e572[0m
[0;34mcontainer.GTF2BED : [0;32mcommunity.wave.seqera.io/library/perl:5.26.2--e6570c5f08d3e12c[0m
[0;34mcontainer.GTF_FILTER : [0;32mcommunity.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a[0m
[0;34mcontainer.GUNZIP : [0;32mcommunity.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc[0m
[0;34mcontainer.HISAT2_ALIGN : [0;32mcommunity.wave.seqera.io/library/hisat2_samtools:9ef5e68250d2aa60[0m
[0;34mcontainer.HISAT2_BUILD : [0;32mcommunity.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5[0m
[0;34mcontainer.HISAT2_EXTRACTSPLICESITES : [0;32mcommunity.wave.seqera.io/library/hisat2:2.2.1--df34d2bb25ac6de5[0m
[0;34mcontainer.KALLISTO_INDEX : [0;32mcommunity.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52[0m
[0;34mcontainer.KALLISTO_QUANT : [0;32mcommunity.wave.seqera.io/library/kallisto:0.51.1--b63691b6841c7a52[0m
[0;34mcontainer.KRAKEN2_KRAKEN2 : [0;32mcommunity.wave.seqera.io/library/kraken2_coreutils_pigz:0892e153c7954635[0m
[0;34mcontainer.MULTIQC : [0;32mcommunity.wave.seqera.io/library/multiqc:1.27--b0d1ffb40dfd9e97[0m
[0;34mcontainer.MULTIQC_CUSTOM_BIOTYPE : [0;32mcommunity.wave.seqera.io/library/python:3.9.5--0ee01a3faebf676a[0m
[0;34mcontainer.PICARD_MARKDUPLICATES : [0;32mcommunity.wave.seqera.io/library/picard:3.1.1--bae6cd265e6bf3d3[0m
[0;34mcontainer.PREPROCESS_TRANSCRIPTS_FASTA_GENCODE : [0;32mcommunity.wave.seqera.io/library/sed:4.7--c9d1b71422302845[0m
[0;34mcontainer.PRESEQ_LCEXTRAP : [0;32mcommunity.wave.seqera.io/library/preseq:3.2.0--2789d8b704b33613[0m
[0;34mcontainer.QUALIMAP_RNASEQ : [0;32mcommunity.wave.seqera.io/library/qualimap:2.3--c1797c2253925b3a[0m
[0;34mcontainer.RSEM_CALCULATEEXPRESSION : [0;32mcommunity.wave.seqera.io/library/rsem_star:5acb4e8c03239c32[0m
[0;34mcontainer.RSEM_MERGE_COUNTS : [0;32mcommunity.wave.seqera.io/library/sed:4.7--c9d1b71422302845[0m
[0;34mcontainer.RSEM_PREPAREREFERENCE : [0;32mcommunity.wave.seqera.io/library/rsem_star:5acb4e8c03239c32[0m
[0;34mcontainer.RSEQC_BAMSTAT : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_INFEREXPERIMENT : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_INNERDISTANCE : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_JUNCTIONANNOTATION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_JUNCTIONSATURATION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_READDISTRIBUTION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_READDUPLICATION : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.RSEQC_TIN : [0;32mcommunity.wave.seqera.io/library/rseqc_r-base:2c6374f25c7b060e[0m
[0;34mcontainer.SALMON_INDEX : [0;32mcommunity.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423[0m
[0;34mcontainer.SALMON_QUANT : [0;32mcommunity.wave.seqera.io/library/salmon:1.10.3--fcd0755dd8abb423[0m
[0;34mcontainer.SAMTOOLS_FLAGSTAT : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_IDXSTATS : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_INDEX : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_SORT : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SAMTOOLS_STATS : [0;32mcommunity.wave.seqera.io/library/htslib_samtools:1.21--6cb89bfd40cbaabf[0m
[0;34mcontainer.SORTMERNA : [0;32mcommunity.wave.seqera.io/library/sortmerna:4.3.7--6502243397c065ba[0m
[0;34mcontainer.STAR_ALIGN : [0;32mcommunity.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829[0m
[0;34mcontainer.STAR_ALIGN_IGENOMES : [0;32mcommunity.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a[0m
[0;34mcontainer.STAR_GENOMEGENERATE : [0;32mcommunity.wave.seqera.io/library/htslib_samtools_star_gawk:311d422a50e6d829[0m
[0;34mcontainer.STAR_GENOMEGENERATE_IGENOMES : [0;32mcommunity.wave.seqera.io/library/star_samtools_gawk:bef5708b1c54889a[0m
[0;34mcontainer.STRINGTIE_STRINGTIE : [0;32mcommunity.wave.seqera.io/library/stringtie:2.2.3--3c30041821e5a79a[0m
[0;34mcontainer.SUBREAD_FEATURECOUNTS : [0;32mcommunity.wave.seqera.io/library/subread:2.0.6--1968a7457b0ed34e[0m
[0;34mcontainer.SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT: [0;32mcommunity.wave.seqera.io/library/bioconductor-summarizedexperiment:1.32.0--13051b66560c2065[0m
[0;34mcontainer.TRIMGALORE : [0;32mcommunity.wave.seqera.io/library/cutadapt_trim-galore_pigz:a98edd405b34582d[0m
[0;34mcontainer.TXIMETA_TXIMPORT : [0;32mcommunity.wave.seqera.io/library/bioconductor-tximeta:1.20.1--cd025af46d4ef23a[0m
[0;34mcontainer.UCSC_BEDCLIP : [0;32mcommunity.wave.seqera.io/library/ucsc-bedclip:377--41de764ea1c26af4[0m
[0;34mcontainer.UCSC_BEDGRAPHTOBIGWIG : [0;32mcommunity.wave.seqera.io/library/ucsc-bedgraphtobigwig:469--f66c00635e28f216[0m
[0;34mcontainer.UMICOLLAPSE : [0;32mcommunity.wave.seqera.io/library/umicollapse:1.1.0--74864b350c72f3a0[0m
[0;34mcontainer.UMITOOLS_DEDUP : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UMITOOLS_EXTRACT : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UMITOOLS_PREPAREFORRSEM : [0;32mcommunity.wave.seqera.io/library/umi_tools:1.1.5--a4e9770134f31e60[0m
[0;34mcontainer.UNTAR : [0;32mcommunity.wave.seqera.io/library/grep_sed_tar:4f61255d5eff93dc[0m
[0;34mlaunchDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/54655b7600b646af862a2f183d5309ad[0m
[0;34mworkDir : [0;32m/home/runner/work/rnaseq/rnaseq/~/tests/54655b7600b646af862a2f183d5309ad/work[0m
[0;34mprojectDir : [0;32m/home/runner/work/rnaseq/rnaseq[0m
[0;34muserName : [0;32mrunner[0m
[0;34mprofile : [0;32mtest,docker[0m
[0;34mconfigFiles : [0;32m/home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/nextflow.config, /home/runner/work/rnaseq/rnaseq/tests/nextflow.config[0m
!! Only displaying parameters that differ from the pipeline defaults !!
-[2m----------------------------------------------------[0m-
* 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: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
'--skip_alignment' parameter has been provided.
Skipping alignment, genome-based quantification and all downstream QC processes.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
WARN: The operator `first` is useless when applied to a value channel which returns a single value by definition
[f1/862ade] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA (gfp.fa.gz)
[e0/2d04de] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF (genes_with_empty_tid.gtf.gz)
[d1/21f8eb] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:KALLISTO_INDEX (transcriptome.fasta)
[58/75d308] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_IAA_30M_REP1)
[d5/89a7cd] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP1)
[ce/92aa27] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (RAP1_UNINDUCED_REP2)
[aa/3b7e82] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP2)
[87/4e4f59] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ (WT_REP1)
[97/4511b5] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX (salmon.tar.gz)
[e1/7cc035] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER (genome.fasta)
[8f/139db7] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_IAA_30M_REP1)
[8c/328481] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP1)
[c7/1952ad] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (RAP1_UNINDUCED_REP2)
[db/aeada5] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP2)
[c9/b17e26] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FQ_LINT (WT_REP1)
[ee/a205aa] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA (null)
[53/73f174] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (RAP1_UNINDUCED_REP2)
[58/8283bf] Submitted process > NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE (WT_REP1)
[a6/b7f8dc] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED (genome_transcriptome.gtf)
[13/a33ebc] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES (genome_transcriptome.fasta)
[a3/322c5d] Submitted process > NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT (null)
WARN: Access to undefined parameter `enable_multiqc_ai` -- Initialise it to a default value eg. `params.enable_multiqc_ai = some_value`
[9b/99a6c3] Submitted process > NFCORE_RNASEQ:RNASEQ:MULTIQC (1)
-[0;35m[nf-core/rnaseq][0;33m Pipeline completed successfully with skipped sampl(es)[0m-
-[0;35m[nf-core/rnaseq][0;31m Please check MultiQC report: 5/5 samples skipped since they failed 10000 trimmed read threshold.[0m-
Nextflow stderr:
Nextflow 24.10.5 is available - Please consider updating your version to it
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