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Update samtools view to add input path(index) (#1539)

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* feat added index as input, to allow module to be used for subsampling

* fix test

* feat added index to meta.yml

* Update modules/samtools/view/meta.yml

feat corrected description of idea pattern file in meta.yml

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
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Lucpen 2022-04-22 10:01:47 +02:00 committed by GitHub
parent f4c69bc427
commit 12afb6b0fa
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3 changed files with 9 additions and 4 deletions
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2
modules/samtools/view/main.nf
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@ -8,7 +8,7 @@ process SAMTOOLS_VIEW {
'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }" 'quay.io/biocontainers/samtools:1.15.1--h1170115_0' }"
input: input:
tuple val(meta), path(input) tuple val(meta), path(input), path(index)
path fasta path fasta
output: output:

4
modules/samtools/view/meta.yml
View file

@ -25,6 +25,10 @@ input:
type: file type: file
description: BAM/CRAM/SAM file description: BAM/CRAM/SAM file
pattern: "*.{bam,cram,sam}" pattern: "*.{bam,cram,sam}"
- index:
type: optional file
description: BAM.BAI/CRAM.CRAI file
pattern: "*.{.bai,.crai}"
- fasta: - fasta:
type: optional file type: optional file
description: Reference file the CRAM was created with description: Reference file the CRAM was created with

7
tests/modules/samtools/view/main.nf
View file

@ -6,7 +6,8 @@ include { SAMTOOLS_VIEW } from '../../../../modules/samtools/view/main.nf'
workflow test_samtools_view { workflow test_samtools_view {
input = [ [ id:'test', single_end:false ], // meta map input = [ [ id:'test', single_end:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true),
[]
] ]
SAMTOOLS_VIEW ( input, [] ) SAMTOOLS_VIEW ( input, [] )
@ -14,8 +15,8 @@ workflow test_samtools_view {
workflow test_samtools_view_cram { workflow test_samtools_view_cram {
input = [ [ id: 'test' ], // meta map input = [ [ id: 'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)
] ]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)