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aws-samples / amazon-omics-tutorials

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manifest generated incorrectly for processes that have 'nfcore' registry #17

Closed nbulsara closed 1 year ago

nbulsara commented 1 year ago

used nf-core/scrnaseq 2.3.0 which has some processes with nfcore/cellranger:7.1.0

The manifest ends up looking like this after running inspect_nf.py

{
    "manifest": [
        "nfcore/cellranger:7.1.0\"\n\n    \n    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {\n        exit 1, \"CELLRANGER_COUN",
        "nfcore/cellranger:7.1.0\"\n\n    \n    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {\n        exit 1, \"CELLRANGER_MKGT",
        "nfcore/cellranger:7.1.0\"\n\n    \n    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {\n        exit 1, \"CELLRANGER_MKRE",
        "nfcore/universc:1.2.5.1\"\n    if (workflow.containerEngine == 'docker')",
        "quay.io/biocontainers/bioconductor-alevinqc:1.12.1--r41h9f5acd7_0",
        "quay.io/biocontainers/fastqc:0.11.9--0",
        "quay.io/biocontainers/gffread:0.12.1--h8b12597_0",
        "quay.io/biocontainers/gffread:0.12.7--hd03093a_1",
        "quay.io/biocontainers/kb-python:0.27.2--pyhdfd78af_0",
        "quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0",
        "quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0",
        "quay.io/biocontainers/multiqc:1.14--pyhdfd78af_0",
        "quay.io/biocontainers/python:3.8.3",
        "quay.io/biocontainers/python:3.9--1",
        "quay.io/biocontainers/scanpy:1.7.2--pyhdfd78af_0",
        "quay.io/biocontainers/simpleaf:0.10.0--h9f5acd7_1",
        "quay.io/biocontainers/star:2.7.10b--h9ee0642_0",
        "satijalab/seurat:4.3.0",
        "ubuntu:20.04"
    ]
}
wleepang commented 1 year ago

This issue is caused by the Groovy if { ... } block that follows the Nextflow container directive