解决： qiime diversity core-metrics-phylogenetic中有一个内容会自动检测GPU，然后调用GPU，如果检测到GPU，但是调用失败则会报错。

在跑命令之前先运行 export UNIFRAC_USE_GPU=N即可使用CPU而不用GPU

解决：在nextflow.config文件中添加nextflowVersion

manifest {
    name            = 'Pacbio'
    author          = """Andreas Wilm, Alexander Peltzer"""
    homePage        = 'https://github.com/PacificBiosciences/HiFi-16S-workflow'
    description     = """Simple bacterial assembly and annotation"""
    mainScript      = 'main.nf'
    nextflowVersion = '!>=23.04.0'
    version         = '2.1.0'
    doi             = '10.5281/zenodo.2669428'
}

添加完即可自动调用nextflow23版本

解决： 在 genostack_core/nextflow/config/nextflow.conf 里面加上

process {
    cpus = 36
    memory = 256.GB
    time = 500.h
    withLabel: sc_tiny {
            cpus = 20
            memory = 200.GB
            time = 500.h }
    withLabel: sc_small {
           cpus = 20
           memory = 200.GB
           time = 500.h }
    withLabel: sc_medium {
          cpus = 20
          memory = 200.GB
          time = 500.h }
    withLabel: mc_small {
          cpus = 20
          memory = 200.GB
          time = 500.h }
    withLabel: mc_medium {
          cpus = 20
          memory = 200.GB
          time = 500.h }
    withLabel: mc_large {
         cpus = 20
         memory = 200.GB
         time = 500.h }
    withLabel: mc_huge {
         cpus = 20
         memory = 200.GB
         time = 500.h }
}

解决：在【modules】-【nf-core】-【strelka】-【germline】-【main.nf】中删除错误文件

mv strelka/results/variants/genome.*.vcf.gz     ${prefix}.genome.vcf.gz
    mv strelka/results/variants/genome.*.vcf.gz.tbi ${prefix}.genome.vcf.gz.tbi
    mv strelka/results/variants/variants.vcf.gz     ${prefix}.variants.vcf.gz
    mv strelka/results/variants/variants.vcf.gz.tbi ${prefix}.variants.vcf.gz.tbi

## 添加这行代码
	rm -rf strelka/results/variants/*

解决：在项目中【modules】-【nf-core】-【fastqc】-【main.nf】中把 fastqc的版本指定。

原来的代码

cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
    END_VERSIONS
    """

修改后的代码

cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        fastqc: 0.12.1
    END_VERSIONS
    """

解决：由于nextflow23.10版本不会生成需要的文件，需要在nextflow23.04版本下运行nextflow run main.nf -profile test,docker -with-dag dag.html -preview 得到dag.html再上传即可

解决：先在服务器里面用命令行运行（命令行运行时会下载需要的插件），运行以后找到~/.nextflow/plugins，然后把plugins压缩打包，并在docker中映射此路径。

同时，需要在项目中的nextflow.config文件中指定插件的版本。如下：

// Nextflow plugins
plugins {
    id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet
    id 'nf-prov@1.2.1'       // Provenance reports for pipeline runs
}