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4398056204
* Add tests and yml file for macs2/callpeak * add format option for macs2 * update macs2/callpeak to accept format argument * update test.yml * update the container version. * try to fix the issue in conda container. * Update conda and containers * Going back to previous container versions Co-authored-by: JoseEspinosa <kadomu@gmail.com>
31 lines
1.4 KiB
Text
31 lines
1.4 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MACS2_CALLPEAK } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
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include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
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include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--format BED --qval 1 --nomodel --extsize 200"] )
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workflow test_macs2_callpeak_bed {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file( params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true)],
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[]]
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MACS2_CALLPEAK_BED ( input, 4000 )
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}
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workflow test_macs2_callpeak {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
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[]]
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MACS2_CALLPEAK ( input, 40000 )
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}
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workflow test_macs2_callpeak_ctrl {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
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[ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
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MACS2_CALLPEAK_CTRL ( input, 40000 )
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}
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