Include all processes in inspect command

[bentsherman]

I found a way to improve the inspect command without using the new script parser -- I just look at all process definitions across all included scripts, regardless of whether they are ever called.

• All processes are included, even if a process is defined but never called by the workflow. Static analysis would be required to extract the process calls from the workflow.

• The process "base name" is used instead of the fully qualified name, and aliases are not included. Static analysis would be required to get the fully qualified name. But I figured the base name is fine because you shouldn't need to specify different containers for different instances of the same process.

I went ahead with this approach because nf-core needs this functionality and I don't know how long it will take to incorporate the new script parser.

Here's the output for rnaseq:

process { withName: 'BBMAP_BBSPLIT' { container = 'quay.io/biocontainers/bbmap:39.10--h92535d8_0' } }
process { withName: 'BEDTOOLS_GENOMECOV' { container = 'quay.io/nf-core/bedtools_coreutils:a623c13f66d5262b' } }
process { withName: 'BRACKEN_BRACKEN' { container = 'quay.io/biocontainers/bracken:2.9--py38h2494328_0' } }
process { withName: 'CAT_FASTQ' { container = 'quay.io/nf-core/coreutils:9.5--ae99c88a9b28c264' } }
process { withName: 'CUSTOM_CATADDITIONALFASTA' { container = 'quay.io/biocontainers/python:3.12' } }
process { withName: 'CUSTOM_GETCHROMSIZES' { container = 'quay.io/biocontainers/samtools:1.21--h50ea8bc_0' } }
process { withName: 'CUSTOM_TX2GENE' { container = 'quay.io/biocontainers/python:3.10.4' } }
process { withName: 'DESEQ2_QC' { container = 'quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' } }
process { withName: 'DUPRADAR' { container = 'quay.io/biocontainers/bioconductor-dupradar:1.32.0--r43hdfd78af_0' } }
process { withName: 'FASTP' { container = 'quay.io/biocontainers/fastp:0.23.4--h5f740d0_0' } }
process { withName: 'FASTQC' { container = 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0' } }
process { withName: 'FQ_SUBSAMPLE' { container = 'quay.io/biocontainers/fq:0.12.0--h9ee0642_0' } }
process { withName: 'GFFREAD' { container = 'quay.io/biocontainers/gffread:0.12.7--hdcf5f25_4' } }
process { withName: 'GTF2BED' { container = 'quay.io/biocontainers/perl:5.26.2' } }
process { withName: 'GTF_FILTER' { container = 'quay.io/biocontainers/python:3.9--1' } }
process { withName: 'GUNZIP' { container = 'quay.io/nf-core/ubuntu:22.04' } }
process { withName: 'HISAT2_ALIGN' { container = 'quay.io/biocontainers/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' } }
process { withName: 'HISAT2_BUILD' { container = 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' } }
process { withName: 'HISAT2_EXTRACTSPLICESITES' { container = 'quay.io/biocontainers/hisat2:2.2.1--h1b792b2_3' } }
process { withName: 'KALLISTO_INDEX' { container = 'quay.io/biocontainers/kallisto:0.51.1--heb0cbe2_0' } }
process { withName: 'KALLISTO_QUANT' { container = 'quay.io/biocontainers/kallisto:0.51.1--heb0cbe2_0' } }
process { withName: 'KRAKEN2_KRAKEN2' { container = 'quay.io/biocontainers/mulled-v2-8706a1dd73c6cc426e12dd4dd33a5e917b3989ae:c8cbdc8ff4101e6745f8ede6eb5261ef98bdaff4-0' } }
process { withName: 'MULTIQC' { container = 'quay.io/biocontainers/multiqc:1.25.1--pyhdfd78af_0' } }
process { withName: 'MULTIQC_CUSTOM_BIOTYPE' { container = 'quay.io/biocontainers/python:3.9--1' } }
process { withName: 'PICARD_MARKDUPLICATES' { container = 'quay.io/biocontainers/picard:3.1.1--hdfd78af_0' } }
process { withName: 'PREPROCESS_TRANSCRIPTS_FASTA_GENCODE' { container = 'quay.io/nf-core/ubuntu:20.04' } }
process { withName: 'PRESEQ_LCEXTRAP' { container = 'quay.io/biocontainers/preseq:3.2.0--hdcf5f25_6' } }
process { withName: 'QUALIMAP_RNASEQ' { container = 'quay.io/biocontainers/qualimap:2.3--hdfd78af_0' } }
process { withName: 'RSEM_CALCULATEEXPRESSION' { container = 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' } }
process { withName: 'RSEM_MERGE_COUNTS' { container = 'quay.io/nf-core/ubuntu:20.04' } }
process { withName: 'RSEM_PREPAREREFERENCE' { container = 'quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0' } }
process { withName: 'RSEQC_BAMSTAT' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'RSEQC_INFEREXPERIMENT' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'RSEQC_INNERDISTANCE' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'RSEQC_JUNCTIONANNOTATION' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'RSEQC_JUNCTIONSATURATION' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'RSEQC_READDISTRIBUTION' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'RSEQC_READDUPLICATION' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'RSEQC_TIN' { container = 'quay.io/biocontainers/rseqc:5.0.3--py39hf95cd2a_0' } }
process { withName: 'SALMON_INDEX' { container = 'quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2' } }
process { withName: 'SALMON_QUANT' { container = 'quay.io/biocontainers/salmon:1.10.3--h6dccd9a_2' } }
process { withName: 'SAMTOOLS_FLAGSTAT' { container = 'quay.io/biocontainers/samtools:1.21--h50ea8bc_0' } }
process { withName: 'SAMTOOLS_IDXSTATS' { container = 'quay.io/biocontainers/samtools:1.21--h50ea8bc_0' } }
process { withName: 'SAMTOOLS_INDEX' { container = 'quay.io/biocontainers/samtools:1.21--h50ea8bc_0' } }
process { withName: 'SAMTOOLS_SORT' { container = 'quay.io/biocontainers/samtools:1.21--h50ea8bc_0' } }
process { withName: 'SAMTOOLS_STATS' { container = 'quay.io/biocontainers/samtools:1.21--h50ea8bc_0' } }
process { withName: 'SORTMERNA' { container = 'quay.io/nf-core/sortmerna:4.3.7--6502243397c065ba' } }
process { withName: 'STAR_ALIGN' { container = 'quay.io/nf-core/star_samtools_htslib_gawk:10c6e8c834460019' } }
process { withName: 'STAR_ALIGN_IGENOMES' { container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' } }
process { withName: 'STAR_GENOMEGENERATE' { container = 'quay.io/nf-core/star_samtools_htslib_gawk:10c6e8c834460019' } }
process { withName: 'STAR_GENOMEGENERATE_IGENOMES' { container = 'quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' } }
process { withName: 'STRINGTIE_STRINGTIE' { container = 'quay.io/biocontainers/stringtie:2.2.3--h43eeafb_0' } }
process { withName: 'SUBREAD_FEATURECOUNTS' { container = 'quay.io/biocontainers/subread:2.0.6--he4a0461_2' } }
process { withName: 'SUMMARIZEDEXPERIMENT_SUMMARIZEDEXPERIMENT' { container = 'quay.io/biocontainers/bioconductor-summarizedexperiment:1.32.0--r43hdfd78af_0' } }
process { withName: 'TRIMGALORE' { container = 'quay.io/biocontainers/trim-galore:0.6.10--hdfd78af_1' } }
process { withName: 'TXIMETA_TXIMPORT' { container = 'quay.io/biocontainers/bioconductor-tximeta:1.20.1--r43hdfd78af_0' } }
process { withName: 'UCSC_BEDCLIP' { container = 'quay.io/biocontainers/ucsc-bedclip:377--h0b8a92a_2' } }
process { withName: 'UCSC_BEDGRAPHTOBIGWIG' { container = 'quay.io/biocontainers/ucsc-bedgraphtobigwig:469--h9b8f530_0' } }
process { withName: 'UMITOOLS_DEDUP' { container = 'quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' } }
process { withName: 'UMITOOLS_EXTRACT' { container = 'quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' } }
process { withName: 'UMITOOLS_PREPAREFORRSEM' { container = 'quay.io/biocontainers/umi_tools:1.1.5--py39hf95cd2a_0' } }
process { withName: 'UNTAR' { container = 'quay.io/nf-core/ubuntu:22.04' } }

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[ewels]

Yesss! 🙏🏻

[bentsherman]

Since the previewAction was created for the inspect command and isn't used for anything else, I use it here to disable the entry workflow execution

Setting the module flag will register the process definitions without running the entry workflow:

nextflow/modules/nextflow/src/main/groovy/nextflow/script/BaseScript.groovy

Lines 159 to 162 in 53d6c61

	final result = runScript()
	if( meta.isModule() ) {
	return result
	}

[pditommaso]

Then I'd say to get rid of previewAction (since it's useless) and use instead ContainerInspectMode that's more explicit about the intent.

[bentsherman]

Okay I tried using the container inspect mode. Don't see a clean way to remove the previewAction altogether as it's a convenient way to pass the callback into the script runner.

[pditommaso]

Looks good! made a couple of minor comments

[pditommaso]

Then I'd say to get rid of previewAction (since it's useless) and use instead ContainerInspectMode that's more explicit about the intent.