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36049bf544
* fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
83 lines
2.3 KiB
Text
83 lines
2.3 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf'
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workflow test_fgbio_fastqtobam_paired_default {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
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]
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]
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FGBIO_FASTQTOBAM ( input )
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}
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workflow test_fgbio_fastqtobam_paired_cram {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
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]
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]
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FGBIO_FASTQTOBAM ( input )
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}
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workflow test_fgbio_fastqtobam_paired_bam {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
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]
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]
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FGBIO_FASTQTOBAM ( input )
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}
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workflow test_fgbio_fastqtobam_single {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
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]
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]
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FGBIO_FASTQTOBAM ( input )
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}
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workflow test_fgbio_fastqtobam_paired_umi {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
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]
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]
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FGBIO_FASTQTOBAM ( input )
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}
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workflow test_fgbio_fastqtobam_paired_custom_samplename {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
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]
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]
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FGBIO_FASTQTOBAM ( input )
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}
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