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A DSL for data-driven computational pipelines
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Nextflow inspect nf-core/rnaseq fails with error #5455

Open mahesh-panchal opened 1 week ago

mahesh-panchal commented 1 week ago

Bug report

nextflow inspect nf-core/rnaseq fails with error:

The following invalid input values have been detected:

You used a core Nextflow option with two hyphens: '--cache'. Please resubmit with '-cache'
* Missing required parameter(s): input

Expected behavior and actual behavior

I expect it to return the container paths or exit with a more suitable error.

Steps to reproduce the problem

nextflow inspect nf-core/rnaseq

Program output

ERROR ~ Validation of pipeline parameters failed!

The following invalid input values have been detected:

You used a core Nextflow option with two hyphens: '--cache'. Please resubmit with '-cache'
* Missing required parameter(s): input

 -- Check script '/Users/mahpa906/.nextflow/assets/nf-core/rnaseq/./subworkflows/local/utils_nfcore_rnaseq_pipeline/../../nf-core/utils_nfschema_plugin/main.nf' at line: 39 or see 'null' file for more details

Environment

Additional context

pditommaso commented 1 week ago

Specify the test profile. notice can be slow: 

$ nextflow inspect nf-core/rnaseq -profile test --outdir results 
{
    "processes": [
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_SCALED",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_CATADDITIONALFASTA",
            "container": "quay.io/biocontainers/python:3.9--1"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDCLIP",
            "container": "quay.io/biocontainers/ucsc-bedclip:377--h0b8a92a_2"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_TRANSCRIPT",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:TXIMETA_TXIMPORT",
            "container": "quay.io/biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_STAR_SALMON",
            "container": "quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:MULTIQC_CUSTOM_BIOTYPE",
            "container": "quay.io/biocontainers/python:3.9--1"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE_LENGTH_SCALED",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:STAR_ALIGN",
            "container": "quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:UNTAR_SALMON_INDEX",
            "container": "quay.io/nf-core/ubuntu:22.04"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:BBMAP_BBSPLIT",
            "container": "quay.io/biocontainers/bbmap:39.01--h5c4e2a8_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_FORWARD:UCSC_BEDGRAPHTOBIGWIG",
            "container": "quay.io/biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:SAMTOOLS_INDEX",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONANNOTATION",
            "container": "quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_FW",
            "container": "quay.io/nf-core/bedtools_coreutils:a623c13f66d5262b"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:BBMAP_BBSPLIT",
            "container": "quay.io/biocontainers/bbmap:39.01--h5c4e2a8_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SALMON_QUANT",
            "container": "quay.io/biocontainers/salmon:1.10.1--h7e5ed60_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:TRIMGALORE",
            "container": "quay.io/biocontainers/trim-galore:0.6.7--hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:FQ_SUBSAMPLE",
            "container": "quay.io/biocontainers/fq:0.9.1--h9ee0642_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDCLIP",
            "container": "quay.io/biocontainers/ucsc-bedclip:377--h0b8a92a_2"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_JUNCTIONSATURATION",
            "container": "quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:CUSTOM_GETCHROMSIZES",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:DUPRADAR",
            "container": "quay.io/biocontainers/bioconductor-dupradar:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:STRINGTIE_STRINGTIE",
            "container": "quay.io/biocontainers/stringtie:2.2.1--hecb563c_2"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:PICARD_MARKDUPLICATES",
            "container": "quay.io/biocontainers/picard:3.1.1--hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:SUBREAD_FEATURECOUNTS",
            "container": "quay.io/biocontainers/subread:2.0.1--hed695b0_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:CAT_FASTQ",
            "container": "quay.io/nf-core/ubuntu:20.04"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE",
            "container": "quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_BAMSTAT",
            "container": "quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SE_GENE",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDUPLICATION",
            "container": "quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_MARKDUPLICATES_PICARD:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:STAR_GENOMEGENERATE",
            "container": "quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_SCALED",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUALIMAP_RNASEQ",
            "container": "quay.io/biocontainers/qualimap:2.3--hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_READDISTRIBUTION",
            "container": "quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BEDTOOLS_GENOMECOV_REV",
            "container": "quay.io/nf-core/bedtools_coreutils:a623c13f66d5262b"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:GTF2BED",
            "container": "quay.io/biocontainers/perl:5.26.2"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:CUSTOM_TX2GENE",
            "container": "quay.io/biocontainers/python:3.9--1"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:GTF_FILTER",
            "container": "quay.io/biocontainers/python:3.9--1"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:DESEQ2_QC_PSEUDO",
            "container": "quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:TXIMETA_TXIMPORT",
            "container": "quay.io/biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:CUSTOM_TX2GENE",
            "container": "quay.io/biocontainers/python:3.9--1"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_TRANSCRIPT",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_FASTQC_UMITOOLS_TRIMGALORE:FASTQC",
            "container": "quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS:FASTQ_SUBSAMPLE_FQ_SALMON:SALMON_QUANT",
            "container": "quay.io/biocontainers/salmon:1.10.1--h7e5ed60_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INFEREXPERIMENT",
            "container": "quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:MULTIQC",
            "container": "quay.io/biocontainers/multiqc:1.24.1--pyhdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_STAR_SALMON:SE_GENE_LENGTH_SCALED",
            "container": "quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT",
            "container": "quay.io/biocontainers/salmon:1.10.1--h7e5ed60_0"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_ADDITIONAL_FASTA",
            "container": "quay.io/nf-core/ubuntu:22.04"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:ALIGN_STAR:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT",
            "container": "quay.io/biocontainers/samtools:1.20--h50ea8bc_0"
        },
        {
            "name": "NFCORE_RNASEQ:PREPARE_GENOME:GUNZIP_GTF",
            "container": "quay.io/nf-core/ubuntu:22.04"
        },
        {
            "name": "NFCORE_RNASEQ:RNASEQ:BEDGRAPH_BEDCLIP_BEDGRAPHTOBIGWIG_REVERSE:UCSC_BEDGRAPHTOBIGWIG",
            "container": "quay.io/biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0"
        }
    ]
}