Nf-core profile ifb_core is now available

You can now use nextflow and nf-core pipeline on IFB core cluster with profile ifb_core

nf-core doc: https://github.com/nf-core/configs/blob/master/docs/ifb_core.md

7 « J'aime »

Bonjour,
J'ai essayé de suivre les instruction pour lancer un run test de la pipeline nf-core/rnaseq depuis mon espace. J'ai essayé les commandes suivantes:
srun --pty bash
module purge
module load nextflow/20.04.1
nextflow run nf-core/rnaseq -r 3.2 -profile test,ifb_core

Néanmoins, j'ai l'erreur suivante:

N E X T F L O W  ~  version 20.04.1
Pulling nf-core/rnaseq ...
downloaded from https://github.com/nf-core/rnaseq.git
Launching `nf-core/rnaseq` [elegant_newton] - revision: b3ff92bc54 [3.2]
Unknown config attribute `params.projectDir` -- check config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config

Je suis bloquée, auriez-vous une idée pour m'aider?
Je vous colle ci-dessous le fichier nextflow.config crée, je ne trouve pas le attribut dont ils parlent.

Merci beaucoup d'avance pour toute aide ou suggestion!

Natalia.

/*
========================================================================================
    nf-core/rnaseq Nextflow config file
========================================================================================
    Default config options for all compute environments
----------------------------------------------------------------------------------------
*/

// Global default params, used in configs
params {

    // Input options
    input                      = null

    // References
    genome                     = null
    transcript_fasta           = null
    additional_fasta           = null
    splicesites                = null
    gtf_extra_attributes       = 'gene_name'
    gtf_group_features         = 'gene_id'
    featurecounts_feature_type = 'exon'
    featurecounts_group_type   = 'gene_biotype'
    gencode                    = false
    save_reference             = false

    // UMI handling
    with_umi                   = false
    umitools_extract_method    = 'string'
    umitools_bc_pattern        = null
    save_umi_intermeds         = false

    // Trimming
    clip_r1                    = null
    clip_r2                    = null
    three_prime_clip_r1        = null
    three_prime_clip_r2        = null
    trim_nextseq               = null
    save_trimmed               = false
    skip_trimming              = false

    // Ribosomal RNA removal
    remove_ribo_rna            = false
    save_non_ribo_reads        = false
    ribo_database_manifest     = "${projectDir}/assets/rrna-db-defaults.txt"

    // Alignment
    aligner                    = 'star_salmon'
    pseudo_aligner             = null
    seq_center                 = null
    bam_csi_index              = false
    star_ignore_sjdbgtf        = false
    salmon_quant_libtype       = null
    hisat2_build_memory        = '200.GB'  // Amount of memory required to build HISAT2 index with splice sites
    stringtie_ignore_gtf       = false
    min_mapped_reads           = 5
    save_merged_fastq          = false
    save_unaligned             = false
    save_align_intermeds       = false
    skip_markduplicates        = false
    skip_alignment             = false

    // QC
    skip_qc                    = false
    skip_bigwig                = false
    skip_stringtie             = false
    skip_fastqc                = false
    skip_preseq                = false
    skip_dupradar              = false
    skip_qualimap              = false
    skip_rseqc                 = false
    skip_biotype_qc            = false
    skip_deseq2_qc             = false
    skip_multiqc               = false
    deseq2_vst                 = false
    rseqc_modules              = 'bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication'

    // Boilerplate options
    outdir                     = './results'
    publish_dir_mode           = 'copy'
    multiqc_config             = null
    multiqc_title              = null
    email                      = null
    email_on_fail              = null
    max_multiqc_email_size     = '25.MB'
    plaintext_email            = false
    monochrome_logs            = false
    help                       = false
    igenomes_base              = 's3://ngi-igenomes/igenomes'
    tracedir                   = "${params.outdir}/pipeline_info"
    igenomes_ignore            = false
    validate_params            = true
    show_hidden_params         = false
    schema_ignore_params       = 'genomes,modules'
    enable_conda               = false
    singularity_pull_docker_container = false

    // Config options
    custom_config_version      = 'master'
    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
    hostnames                  = [:]
    config_profile_name        = null
    config_profile_description = null
    config_profile_contact     = null
    config_profile_url         = null

    // Defaults only, expecting to be overwritten
    max_memory                 = '128.GB'
    max_cpus                   = 16
    max_time                   = '240.h'
}

// Load base.config by default for all pipelines
includeConfig 'conf/base.config'

// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'

// Load nf-core custom profiles from different Institutions
try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}

// Load nf-core/rnaseq custom config
try {
    includeConfig "${params.custom_config_base}/pipeline/rnaseq.config"
} catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config/rnaseq profiles: ${params.custom_config_base}/pipeline/rnaseq.config")
}

// Load igenomes.config if required
if (!params.igenomes_ignore) {
    includeConfig 'conf/igenomes.config'
} else {
    params.genomes = [:]
}

profiles {
    debug { process.beforeScript = 'echo $HOSTNAME' }
    conda {
        params.enable_conda    = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    docker {
        docker.enabled         = true
        docker.userEmulation   = true
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    singularity {
        singularity.enabled    = true
        singularity.autoMounts = true
        docker.enabled         = false
        podman.enabled         = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    podman {
        podman.enabled         = true
        docker.enabled         = false
        singularity.enabled    = false
        shifter.enabled        = false
        charliecloud.enabled   = false
    }
    shifter {
        shifter.enabled        = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        charliecloud.enabled   = false
    }
    charliecloud {
        charliecloud.enabled   = true
        docker.enabled         = false
        singularity.enabled    = false
        podman.enabled         = false
        shifter.enabled        = false
    }
    test      { includeConfig 'conf/test.config'      }
    test_full { includeConfig 'conf/test_full.config' }
}

// Export these variables to prevent local Python/R libraries from conflicting with those in the container
env {
    PYTHONNOUSERSITE = 1
    R_PROFILE_USER   = "/.Rprofile"
    R_ENVIRON_USER   = "/.Renviron"
}

def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
    enabled = true
    file    = "${params.tracedir}/execution_timeline_${trace_timestamp}.html"
}
report {
    enabled = true
    file    = "${params.tracedir}/execution_report_${trace_timestamp}.html"
}
trace {
    enabled = true
    file    = "${params.tracedir}/execution_trace_${trace_timestamp}.txt"
}
dag {
    enabled = true
    file    = "${params.tracedir}/pipeline_dag_${trace_timestamp}.svg"
}

manifest {
    name            = 'nf-core/rnaseq'
    author          = 'Phil Ewels, Rickard Hammarén'
    homePage        = 'https://github.com/nf-core/rnaseq'
    description     = 'Nextflow RNA-Seq analysis pipeline, part of the nf-core community.'
    mainScript      = 'main.nf'
    nextflowVersion = '!>=21.04.0'
    version         = '3.2'
}

// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
    if (type == 'memory') {
        try {
            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
                return params.max_memory as nextflow.util.MemoryUnit
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'time') {
        try {
            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
                return params.max_time as nextflow.util.Duration
            else
                return obj
        } catch (all) {
            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
            return obj
        }
    } else if (type == 'cpus') {
        try {
            return Math.min( obj, params.max_cpus as int )
        } catch (all) {
            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
            return obj
        }
    }
}

Bonjour,

projectDir n'est effectivement pas un params, mais une variable interne à Nextflow devant normalement pointer vers la base du repo.
On a normalement pas de soucis avec son utilisation, je vais me pencher sur la question.

Pouvez-vous joindre le fichier .nexflow.log ?

Bonjour @npinzonrestrepo

Avez-vous pu résoudre le problème ? Pouvez-vous nous joindre le fichier log de nextflow ( .nexflow.log) ?

Bonjour,

Désolée pour le délai. Je n'ai aps résolu le problème. Voic le fichier .log de nextflow

Jul-05 13:14:47.820 [main] DEBUG nextflow.cli.Launcher - $> nextflow run nf-core/rnaseq -r 3.0 -profile test,ifb_core
Jul-05 13:14:47.920 [main] INFO  nextflow.cli.CmdRun - N E X T F L O W  ~  version 20.04.1
Jul-05 13:14:48.581 [main] DEBUG nextflow.scm.AssetManager - Git config: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Jul-05 13:14:48.595 [main] DEBUG nextflow.scm.AssetManager - Git config: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Jul-05 13:14:48.982 [main] DEBUG nextflow.scm.AssetManager - Git config: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/.git/config; branch: master; remote: origin; url: https://github.com/nf-core/rnaseq.git
Jul-05 13:14:48.982 [main] INFO  nextflow.cli.CmdRun - Launching `nf-core/rnaseq` [focused_kirch] - revision: 3643a94411 [3.0]
Jul-05 13:14:49.575 [main] DEBUG nextflow.config.ConfigBuilder - Found config base: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
Jul-05 13:14:49.575 [main] DEBUG nextflow.config.ConfigBuilder - Found config local: /shared/ifbstor1/home/npinzonrestrepo/nextflow.config
Jul-05 13:14:49.576 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
Jul-05 13:14:49.576 [main] DEBUG nextflow.config.ConfigBuilder - Parsing config file: /shared/ifbstor1/home/npinzonrestrepo/nextflow.config
Jul-05 13:14:49.584 [main] DEBUG nextflow.config.ConfigBuilder - Applying config profile: `test,ifb_core`
Jul-05 13:14:50.281 [main] DEBUG nextflow.config.ConfigBuilder - In the following config object the attribute `params.projectDir` is empty:
  input='https://raw.githubusercontent.com/nf-core/test-datasets/rnaseq/samplesheet/samplesheet.csv'
  public_data_ids=''
  skip_sra_fastq_download=false
  genome=''
  transcript_fasta='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/transcriptome.fasta'
  additional_fasta='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/gfp.fa.gz'
  splicesites=''
  gtf_extra_attributes='gene_name'
  gtf_group_features='gene_id'
  gtf_count_type='exon'
  gtf_group_features_type='gene_biotype'
  gencode=false
  save_reference=false
  with_umi=false
  umitools_extract_method='string'
  umitools_bc_pattern='NNNN'
  save_umi_intermeds=false
  clip_r1=0
  clip_r2=0
  three_prime_clip_r1=0
  three_prime_clip_r2=0
  trim_nextseq=0
  save_trimmed=false
  skip_trimming=false
  remove_ribo_rna=false
  save_non_ribo_reads=false
  ribo_database_manifest=[:]/assets/rrna-db-defaults.txt
  aligner='star_salmon'
  pseudo_aligner='salmon'
  seq_center=''
  star_ignore_sjdbgtf=false
  hisat_build_memory=200
  stringtie_ignore_gtf=false
  min_mapped_reads=5
  save_merged_fastq=false
  save_unaligned=false
  save_align_intermeds=false
  skip_markduplicates=false
  skip_alignment=false
  skip_qc=false
  skip_bigwig=false
  skip_stringtie=false
  skip_fastqc=false
  skip_preseq=false
  skip_dupradar=false
  skip_qualimap=false
  skip_rseqc=false
  skip_biotype_qc=false
  skip_deseq2_qc=false
  skip_multiqc=false
  deseq2_vst=false
  rseqc_modules='bam_stat,inner_distance,infer_experiment,junction_annotation,junction_saturation,read_distribution,read_duplication'
  enable_conda=false
  clusterOptions=''
  outdir='./results'
  publish_dir_mode='copy'
  multiqc_config=''
  multiqc_title=''
  email=''
  email_on_fail=''
  max_multiqc_email_size='25.MB'
  plaintext_email=false
  monochrome_logs=false
  help=false
  igenomes_base='s3://ngi-igenomes/igenomes/'
  tracedir=./results/pipeline_info
  igenomes_ignore=true
  singularity_pull_docker_container=false
  custom_config_version='master'
  custom_config_base=https://raw.githubusercontent.com/nf-core/configs/master
  hostnames=['binac':['.binac.uni-tuebingen.de'], 'cbe':['.cbe.vbc.ac.at'], 'cfc':['.hpc.uni-tuebingen.de'], 'crick':['.thecrick.org'], 'icr_davros':['.davros.compute.estate'], 'imperial':['.hpc.ic.ac.uk'], 'imperial_mb':['.hpc.ic.ac.uk'], 'genotoul':['.genologin1.toulouse.inra.fr', '.genologin2.toulouse.inra.fr'], 'genouest':['.genouest.org'], 'uppmax':['.uppmax.uu.se'], 'utd_ganymede':['ganymede.utdallas.edu'], 'utd_sysbio':['sysbio.utdallas.edu']]
  config_profile_description='Minimal test dataset to check pipeline function'
  config_profile_contact='https://community.france-bioinformatique.fr'
  config_profile_url='https://www.france-bioinformatique.fr/'
  max_memory=6 GB
  max_cpus=2
  max_time=2d
  modules {
  	sra_ids_to_runinfo {
  		publish_dir='public_data'
  		publish_files=['tsv':'runinfo']
  	}
  	sra_runinfo_to_ftp {
  		publish_dir='public_data'
  		publish_files=['tsv':'runinfo']
  	}
  	sra_fastq_ftp {
  		publish_dir='public_data'
  		publish_files=['fastq.gz':'', 'md5':'md5']
  	}
  	sra_to_samplesheet {
  		publish_dir='public_data'
  		publish_files=false
  	}
  	sra_merge_samplesheet.publish_dir='public_data'
  	gffread {
  		args='--keep-exon-attrs -F -T'
  		publish_dir='genome'
  	}
  	cat_fastq.publish_dir='fastq'
  	fastqc.args='--quiet'
  	trimgalore {
  		args='--fastqc'
  		publish_files=['txt':'', 'html':'fastqc', 'zip':'fastqc']
  	}
  	umitools_extract {
  		args=''
  		publish_files=['log':'']
  	}
  	sortmerna {
  		args='--num_alignments 1 --fastx -v'
  		publish_files=['log':'']
  	}
  	star_genomegenerate.publish_dir='genome/index'
  	star_align {
  		args='--quantMode TranscriptomeSAM --twopassMode Basic --outSAMtype BAM Unsorted --readFilesCommand zcat --runRNGseed 0 --outFilterMultimapNmax 20 --alignSJDBoverhangMin 1 --outSAMattributes NH HI AS NM MD --quantTranscriptomeBan Singleend'
  		publish_dir=star_salmon
  		publish_files=['out':'log', 'tab':'log']
  	}
  	star_salmon_quant.publish_dir=star_salmon
  	star_salmon_tximport {
  		publish_dir=star_salmon
  		publish_by_id=true
  	}
  	star_salmon_merge_counts.publish_dir=star_salmon
  	hisat2_build.publish_dir='genome/index'
  	hisat2_align {
  		args='--met-stderr --new-summary --dta'
  		publish_files=['log':'log']
  	}
  	rsem_preparereference {
  		args='--star'
  		publish_dir='genome/index'
  		args2='--genomeSAindexNbases 7'
  	}
  	rsem_calculateexpression {
  		args='--star --star-output-genome-bam --star-gzipped-read-file --estimate-rspd --seed 1'
  		publish_files=['log':'log', 'stat':'', 'results':'']
  		publish_dir=star_salmon
  	}
  	rsem_merge_counts.publish_dir=star_salmon
  	samtools_sort {
  		suffix='.sorted'
  		publish_files=['stats':'samtools_stats', 'flagstat':'samtools_stats', 'idxstats':'samtools_stats']
  		publish_dir=star_salmon
  	}
  	salmon_index {
  		args=''
  		publish_dir='genome/index'
  	}
  	salmon_quant.args=''
  	salmon_tximport.publish_by_id=true
  	salmon_merge_counts.publish_dir=
  	preseq_lcextrap {
  		args='-verbose -bam -seed 1 -seg_len 100000000'
  		publish_files=['txt':'', 'log':'log']
  		publish_dir=star_salmon/preseq
  	}
  	umitools_dedup {
  		publish_files=['tsv':'umitools']
  		suffix='.umi_dedup.sorted'
  		publish_dir=star_salmon
  	}
  	picard_markduplicates {
  		args='ASSUME_SORTED=true REMOVE_DUPLICATES=false VALIDATION_STRINGENCY=LENIENT TMP_DIR=tmp'
  		suffix='.markdup.sorted'
  		publish_files=['bam':'', 'metrics.txt':'picard_metrics']
  		publish_dir=star_salmon
  	}
  	picard_markduplicates_samtools {
  		suffix='.markdup.sorted'
  		publish_files=['bai':'', 'stats':'samtools_stats', 'flagstat':'samtools_stats', 'idxstats':'samtools_stats']
  		publish_dir=star_salmon
  	}
  	stringtie {
  		args='-v'
  		publish_dir=star_salmon/stringtie
  	}
  	subread_featurecounts {
  		args='-B -C'
  		publish_dir=star_salmon/featurecounts
  	}
  	multiqc_custom_biotype.publish_dir=star_salmon/featurecounts
  	bedtools_genomecov.publish_files=false
  	ucsc_bedclip {
  		suffix='.clip'
  		publish_files=false
  	}
  	ucsc_bedgraphtobigwig.publish_dir=star_salmon/bigwig
  	deseq2_qc {
  		args='--id_col 1 --sample_suffix \'\' --outprefix deseq2'
  		publish_files=['RData':'', 'pca.vals.txt':'', 'plots.pdf':'', 'sample.dists.txt':'', 'size_factors':'', 'log':'']
  		publish_dir=star_salmon/deseq2_qc
  	}
  	qualimap_rnaseq.publish_dir=star_salmon/qualimap
  	dupradar {
  		publish_files=['Dens.pdf':'scatter_plot', 'Boxplot.pdf':'box_plot', 'Hist.pdf':'histogram', 'Matrix.txt':'gene_data', 'slope.txt':'intercepts_slope']
  		publish_dir=star_salmon/dupradar
  	}
  	rseqc_bamstat.publish_dir=star_salmon/rseqc/bam_stat
  	rseqc_innerdistance {
  		publish_files=['txt':'txt', 'pdf':'pdf', '.r':'rscript']
  		publish_dir=star_salmon/rseqc/inner_distance
  	}
  	rseqc_inferexperiment.publish_dir=star_salmon/rseqc/infer_experiment
  	rseqc_junctionannotation {
  		publish_files=['pdf':'pdf', '.r':'rscript', 'bed':'bed', 'xls':'xls', 'log':'log']
  		publish_dir=star_salmon/rseqc/junction_annotation
  	}
  	rseqc_junctionsaturation {
  		publish_files=['pdf':'pdf', '.r':'rscript']
  		publish_dir=star_salmon/rseqc/junction_saturation
  	}
  	rseqc_readdistribution.publish_dir=star_salmon/rseqc/read_distribution
  	rseqc_readduplication {
  		publish_files=['pdf':'pdf', '.r':'rscript', 'xls':'xls']
  		publish_dir=star_salmon/rseqc/read_duplication
  	}
  	multiqc {
  		args=''
  		publish_dir=multiqc/star_salmon
  	}
  }
  genomes=[:]
  config_profile_name='Test profile'
  fasta='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genome.fa'
  gtf='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gtf.gz'
  gff='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/genes.gff.gz'
  hisat2_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/hisat2.tar.gz'
  star_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/star.tar.gz'
  salmon_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/salmon.tar.gz'
  rsem_index='https://github.com/nf-core/test-datasets/raw/rnaseq/reference/rsem.tar.gz'

Jul-05 13:14:50.286 [main] ERROR nextflow.cli.Launcher - Unknown config attribute `params.projectDir` -- check config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
nextflow.exception.ConfigParseException: Unknown config attribute `params.projectDir` -- check config file: /shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/nextflow.config
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
	at java.base/java.lang.reflect.Constructor.newInstance(Constructor.java:490)
	at org.codehaus.groovy.reflection.CachedConstructor.invoke(CachedConstructor.java:80)
	at org.codehaus.groovy.reflection.CachedConstructor.doConstructorInvoke(CachedConstructor.java:74)
	at org.codehaus.groovy.runtime.callsite.ConstructorSite$ConstructorSiteNoUnwrap.callConstructor(ConstructorSite.java:84)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallConstructor(CallSiteArray.java:59)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:237)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callConstructor(AbstractCallSite.java:249)
	at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:405)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184)
	at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy:407)
	at nextflow.config.ConfigBuilder.validate(ConfigBuilder.groovy)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
	at nextflow.config.ConfigBuilder.merge0(ConfigBuilder.groovy:372)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:184)
	at nextflow.config.ConfigBuilder.buildConfig0(ConfigBuilder.groovy:321)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:176)
	at nextflow.config.ConfigBuilder.buildGivenFiles(ConfigBuilder.groovy:287)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:566)
	at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:190)
	at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:58)
	at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCallCurrent(CallSiteArray.java:51)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:156)
	at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:168)
	at nextflow.config.ConfigBuilder.buildConfigObject(ConfigBuilder.groovy:659)
	at nextflow.config.ConfigBuilder.build(ConfigBuilder.groovy:672)
	at nextflow.script.ScriptRunner.<init>(ScriptRunner.groovy:84)
	at nextflow.cli.CmdRun.run(CmdRun.groovy:254)
	at nextflow.cli.Launcher.run(Launcher.groovy:460)
	at nextflow.cli.Launcher.main(Launcher.groovy:642)

Bonjour Natalia,

Comme discuté sur ce post: https://community.france-bioinformatique.fr/t/erreur-lancement-nf-core-rnaseq/, en palliatif, pouvez-vous essayer en exportant la variable d'environnement projectDir:

export projectDir=/shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/

Et/Ou avec la version 21.04 de NextFlow:

export JAVA_LD_LIBRARY_PATH=/shared/ifbstor1/software/miniconda/envs/nextflow-21.04.0/lib/server
export JAVA_HOME=/shared/ifbstor1/software/miniconda/envs/nextflow-21.04.0
module load nextflow/21.04.0 

Bonjour dbenaben,

Merci beaucoup! J'ai eu le même résultat que dans le post https://community.france-bioinformatique.fr/t/erreur-lancement-nf-core-rnaseq/

Avec la version 20.04.1 j'obtiens ceci:

 N E X T F L O W  ~  version 20.04.1
Launching `nf-core/rnaseq` [clever_boyd] - revision: b3ff92bc54 [3.2]
WARN: DSL 2 IS AN EXPERIMENTAL FEATURE UNDER DEVELOPMENT -- SYNTAX MAY CHANGE IN FUTURE RELEASE
No such variable: enable

 -- Check script '/shared/home/npinzonrestrepo/.nextflow/assets/nf-core/rnaseq/main.nf' at line: 12 or see '.nextflow.log' file for more details

En chargenat les variables d'environnement et la version 21.04 de Nextflow, la pipeline test tourne.

Cependant, elle s'arrête à cause d'une erreur dans le processus DESEQ2_QC_SALMON. Si je vais dans le répertoire de travail, dans le command.log, l'information sur l'erreur produite est:

Error in validObject(.Object) :
  invalid class "DESeqDataSet" object: superclass "RectangularData" not defined in the environment of the object's class

Auriez-vous peut-être une suggestion?

Voici ce que dit le .nextflow.log:

Jul-23 15:17:44.130 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON'

Caused by:
  Process `NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_SALMON` terminated with an error exit status (1)

Command executed:

  deseq2_qc.r \
      --count_file salmon.merged.gene_counts_length_scaled.tsv \
      --outdir ./ \
      --cores 2 \
      --id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 3

  if [ -f "R_sessionInfo.log" ]; then
      sed "s/deseq2_pca/salmon_deseq2_pca/g" <deseq2_pca_header.txt >tmp.txt
      sed -i -e "s/DESeq2 PCA/SALMON DESeq2 PCA/g" tmp.txt
      cat tmp.txt *.pca.vals.txt > salmon.pca.vals_mqc.tsv

      sed "s/deseq2_clustering/salmon_deseq2_clustering/g" <deseq2_clustering_header.txt >tmp.txt
      sed -i -e "s/DESeq2 sample/SALMON DESeq2 sample/g" tmp.txt
      cat tmp.txt *.sample.dists.txt > salmon.sample.dists_mqc.tsv
  fi

  Rscript -e "library(DESeq2); write(x=as.character(packageVersion('DESeq2')), file='deseq2.version.txt')"

Command exit status:
  1

Command output:
  (empty)

Command error:
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which, which.max, which.min


  Attaching package: 'S4Vectors'

  The following object is masked from 'package:base':

      expand.grid

Je dois avouer que cela me dépasse.
Peut-être que la @team.workflow aura plus d'idées ?

@npinzonrestrepo Pas de soucis de mon coté quand je reproduis le test.
Pourriez-vous créer une issue sur GitHub: Issues · nf-core/rnaseq · GitHub
En specifiant les profils utilisés, la version de Nextflow, et joindre les fichiers .command.log .command.err du repertoire de travail, ainsi que le fichier .nextflow.log ?
Je pense que les devs du pipeline seront plus à même de pouvoir réagir à ce bug.

merci @maxulysse et @dbenaben !
Je vais faire ça, mais avant, je constate qu'il y a ce warning sur mon .command.err:

[33mWARNING:[0m Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container

Il y aurait peut-être un conflit sur, peut-être, la version de singularity dans mon cas?

[33mWARNING:[0m Skipping mount /usr/local/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min


Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from 'package:base':

    aperm, apply, rowsum

converting counts to integer mode
Error in validObject(.Object) : 
  invalid class "DESeqDataSet" object: superclass "RectangularData" not defined in the environment of the object's class
Calls: DESeqDataSetFromMatrix ... DESeqDataSet -> new -> initialize -> initialize -> validObject
Execution halted


Le WARNING est pour moi sans conséquence et n'est probablement pas lié à l'erreur invalid class "DESeqDataSet".

Je pense comme @dbenaben

Merci beaucoup @maxulysse et @dbenaben !!

J'ai demandé l'aide du dev principal sur l'issue (error running nf-core rnaseq test pipeline · Issue #679 · nf-core/rnaseq · GitHub)

1 « J'aime »

Bonjour @maxulysse et @dbenaben, j'ai finalement résolue le problème.
J'ai caché mon ~/R et maintenant ça tourne bien. Apparamment la pipeline allait le chercher :blush: .
Merci encore pour votre aide!