mirror of
https://github.com/MillironX/nf-core_modules.git
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572abb00b3
* Remove def from module options definition in main
* Fix bismark_deduplicate tests
* Fix bwameth_align tests
* Fixing gatk4 conda tests ("=" instead of ':' in build id)
* Same as previous commit (Fix gatk4 test)
* Fix qualimap bamqc test (no md5 check for pngs)
* Fix seqkit split2 tests. Changed to new test data
* Fix samtools tests. Some were missing initOptions include
* Removing TOOL SUBTOOL template module since now it is included on tools repo
55 lines
2.1 KiB
Text
55 lines
2.1 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_LENGTH } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-length 8K'] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_SIZE } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-size 50' ] )
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include { SEQKIT_SPLIT2 as SEQKIT_SPLIT2_PART } from '../../../../software/seqkit/split2/main.nf' addParams( options: ['args': '--by-part 3'] )
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workflow test_seqkit_split2_single_end_length {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_LENGTH ( input )
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}
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workflow test_seqkit_split2_single_end_size {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_SIZE ( input )
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}
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workflow test_seqkit_split2_single_end_part {
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def input = []
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input = [ [ id:'test', single_end:true ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_PART ( input )
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}
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workflow test_seqkit_split2_paired_end_length {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_[1-2].fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_LENGTH ( input )
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}
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workflow test_seqkit_split2_paired_end_size {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}//tests/data/genomics/sarscov2/fastq/test_[1-2].fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_SIZE ( input )
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}
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workflow test_seqkit_split2_paired_end_part {
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def input = []
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input = [ [ id:'test', single_end:false ], // meta map
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file("${launchDir}//tests/data/genomics/sarscov2/fastq/test_[1-2].fastq.gz", checkIfExists: true) ]
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SEQKIT_SPLIT2_PART ( input )
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}
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