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Merge pull request #141 from nf-core/minimap-patch

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Remove necessity of patch
This commit is contained in:
James A. Fellows Yates 2022-10-11 12:46:26 +02:00 committed by GitHub
commit f25ee17fcf
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4 changed files with 5 additions and 26 deletions
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3
modules.json
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@ -119,8 +119,7 @@
},
"minimap2/index": {
"branch": "master",
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905",
"patch": "modules/nf-core/minimap2/index/minimap2-index.diff"
"git_sha": "5e34754d42cd2d5d248ca8673c0a53cdf5624905"
},
"motus/merge": {
"branch": "master",

6
modules/nf-core/minimap2/index/main.nf generated
View file

@ -7,11 +7,11 @@ process MINIMAP2_INDEX {
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
input:
path fasta
tuple val(meta), path(fasta)
output:
path "*.mmi" , emit: index
path "versions.yml" , emit: versions
tuple val(meta), path("*.mmi"), emit: index
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when

20
modules/nf-core/minimap2/index/minimap2-index.diff generated
View file

@ -1,20 +0,0 @@
Changes in module 'nf-core/minimap2/index'
--- modules/nf-core/minimap2/index/main.nf
+++ modules/nf-core/minimap2/index/main.nf
@@ -7,11 +7,11 @@
'quay.io/biocontainers/minimap2:2.21--h5bf99c6_0' }"
input:
- tuple val(meta), path(fasta)
+ path fasta
output:
- tuple val(meta), path("*.mmi"), emit: index
- path "versions.yml" , emit: versions
+ path "*.mmi" , emit: index
+ path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
************************************************************

2
subworkflows/local/longread_hostremoval.nf
View file

@ -18,7 +18,7 @@ workflow LONGREAD_HOSTREMOVAL {
ch_multiqc_files = Channel.empty()
if ( !params.longread_hostremoval_index ) {
ch_minimap2_index = MINIMAP2_INDEX ( reference ).index
ch_minimap2_index = MINIMAP2_INDEX ( [ [], reference ] ).index.map { it[1] }
ch_versions = ch_versions.mix( MINIMAP2_INDEX.out.versions )
} else {
ch_minimap2_index = index