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fix: picard filtersamreads input (#610)

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* Move readlist into same input channel as bam

* Update test reflecting input restructuring

* Update tests/modules/picard/filtersamreads/main.nf

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>

* fix test

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
James A. Fellows Yates 2021-07-22 12:19:51 +02:00 committed by GitHub
parent 3cc43838e1
commit 553f51d6bf
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2 changed files with 10 additions and 6 deletions
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3
modules/picard/filtersamreads/main.nf
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@ -19,9 +19,8 @@ process PICARD_FILTERSAMREADS {
} }
input: input:
tuple val(meta), path(bam) tuple val(meta), path(bam), path(readlist)
val filter val filter
path readlist
output: output:
tuple val(meta), path("*.bam"), emit: bam tuple val(meta), path("*.bam"), emit: bam

13
tests/modules/picard/filtersamreads/main.nf
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@ -13,15 +13,20 @@ workflow test_picard_filtersamreads {
filter = 'includeAligned' filter = 'includeAligned'
PICARD_SORTSAM ( input, sort_order ) PICARD_SORTSAM ( input, sort_order )
PICARD_FILTERSAMREADS ( PICARD_SORTSAM.out.bam, filter, [] ) PICARD_SORTSAM.out.bam
.map {
[ it[0], it[1], [] ]
}
.set{ ch_sorted_for_filtersamreads }
PICARD_FILTERSAMREADS ( ch_sorted_for_filtersamreads, filter )
} }
workflow test_picard_filtersamreads_readlist { workflow test_picard_filtersamreads_readlist {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ] file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_single_end_bam_readlist_txt'], checkIfExists: true) ]
filter = 'includeReadList' filter = 'includeReadList'
readlist = file(params.test_data['sarscov2']['illumina']['test_single_end_bam_readlist_txt'], checkIfExists: true)
PICARD_FILTERSAMREADS ( input, filter, readlist ) PICARD_FILTERSAMREADS ( input, filter )
} }