mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
b399f22af2
* add pydamage module * remove TODOs * split module by subcommands * update version parsing * remove forgotten TODOs * update module names * remove old holistic module * Update modules/pydamage/analyze/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add keywords * update resource requirement * Update modules/pydamage/filter/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/pydamage/filter/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * merge from upstream * update pydamage from upstream * add freebayes * update pydamage test from upstream * fix meta.yml * update functions.nf * update test.yml * update version parsing * update version parsing * fix indentation * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs * Update modules/freebayes/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add bed test * add metabat2 module * only freebayes * remove metabat2 * update md5sum because of vcf including date of the day * add keyword * rescue conflicted files * attempt to fix ECLint * add pytest workflow for metabat * remove - * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/metabat2/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/metabat2/jgisummarizebamcontigdepths/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add optional inputs/outpus * remove trailing whitespace * first cmseq commit * compressing and removing not reproducible md5sums * save intermediate work * follow symlinks while decompressing * add cmseq/polymut * add polymut * add extra test with optional input file * remove metabat2 * Update modules/cmseq/polymut/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * fix file extension * Update modules/cmseq/polymut/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * add test without bam index * split tests in workflows * answer PR review * report version from variable Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
38 lines
1.5 KiB
Text
38 lines
1.5 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { CMSEQ_POLYMUT } from '../../../../modules/cmseq/polymut/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_cmseq_polymut_1 {
|
|
|
|
input_1 = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
[],
|
|
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
|
|
[] ]
|
|
|
|
CMSEQ_POLYMUT( input_1 )
|
|
|
|
}
|
|
|
|
workflow test_cmseq_polymut_2 {
|
|
input_2 = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
|
|
[] ]
|
|
|
|
CMSEQ_POLYMUT( input_2 )
|
|
}
|
|
|
|
workflow test_cmseq_polymut_3 {
|
|
input_3 = [ [ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), ]
|
|
|
|
CMSEQ_POLYMUT( input_3 )
|
|
}
|
|
|