add estimatemutationalburden as module

[famosab]

PR checklist

Closes #XXX
Replaces #3530

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
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• Emit the versions.yml file.
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[famosab]

I will create the proper test vcf file by running the processes because thats probably a very long setup block :D

[famosab]

That means running the setup locally and the upload the file to test-datasets.

   setup {
        run("VARLOCIRAPTOR_ESTIMATEALIGNMENTPROPERTIES") {
            script "../../estimatealignmentproperties/main.nf"
            process {
                """
                input[0] = [
                    [id:'test_normal'],
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true),
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true),
                    ]
                input[1] = [
                    [id:'test'],
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
                    ]
                input[2] = [
                    [id:'test'],
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
                    ]
                """
            }
        }

        run("VARLOCIRAPTOR_PREPROCESS" ) {
            script "../../preprocess/main.nf"
            process {
                """
                input[0] = Channel.of([
                    [id:'test_normal'],
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists:true),
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists:true),
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists:true),
                    ]).collect().join(VARLOCIRAPTOR_ESTIMATEALIGNMENTPROPERTIES.out.alignment_properties_json)
                input[1] = [
                    [id:'test'],
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists:true)
                    ]
                input[2] = [
                    [id:'test'],
                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists:true)
                    ]
                """
            }
        }

        run("VARLOCIRAPTOR_CALLVARIANTS") {
            script "../../callvariants/main.nf"
            process {
                """
                input[0] = VARLOCIRAPTOR_PREPROCESS.out.bcf.map{meta1,vcf->[meta1,vcf,[]]}
                input[1] = Channel.of(file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/varlociraptor/scenario.yml', checkIfExists:true))
                input[2] = "normal"
                """
            }
        }

        run("BCFTOOLS_VIEW") {
            script "../../../bcftools/view/main.nf"
            process {
                """
                input[0] = VARLOCIRAPTOR_CALLVARIANTS.out.bcf.map{it -> [ it[0], it[1], [] ]}
                input[1] = []
                input[2] = []
                input[3] = []
                """
            }
        }

        run("SNPEFF_DOWNLOAD") {
            script "../../../snpeff/download/main.nf"
            process {
                """
                input[0] = Channel.of([[id:'GRCh38.105'], 'GRCh38.105'])
                """
            }
        }


        run("SNPEFF_SNPEFF") {
            script "../../../snpeff/snpeff/main.nf"
            process {
                """
                input[0] = BCFTOOLS_VIEW.out.vcf
                input[1] = 'GRCh38.105'
                input[2] = SNPEFF_DOWNLOAD.out.cache
                """
            }
        }

    }

[famosab]

Getting this error:

Error: unable to estimate TMB because no valid records were found in the given BCF/VCF