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Proof of concept: Diff override for bismark alignment #2

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Proof of concept: Diff override for bismark alignment #2

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7 changes: 5 additions & 2 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,10 @@
"repos": {
"nf-core/modules": {
"bismark/align": {
"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae",
"patches": [
"modules/nf-core/modules/bismark/align/index_per_sample.diff"
]
},
"bismark/deduplicate": {
"git_sha": "3aacd46da2b221ed47aaa05c413a828538d2c2ae"
Expand Down Expand Up @@ -68,4 +71,4 @@
}
}
}
}
}
14 changes: 14 additions & 0 deletions modules/nf-core/modules/bismark/align/index_per_sample.diff
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Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
diff --git a/modules/nf-core/modules/bismark/align/main.nf b/modules/nf-core/modules/bismark/align/main.nf
index aa4879b..c03a6f9 100644
--- a/modules/nf-core/modules/bismark/align/main.nf
+++ b/modules/nf-core/modules/bismark/align/main.nf
@@ -19,8 +19,7 @@ process BISMARK_ALIGN {
}

input:
- tuple val(meta), path(reads)
- path index
+ tuple val(meta), path(reads), path(index)

output:
tuple val(meta), path("*bam") , emit: bam
3 changes: 1 addition & 2 deletions modules/nf-core/modules/bismark/align/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,7 @@ process BISMARK_ALIGN {
}

input:
tuple val(meta), path(reads)
path index
tuple val(meta), path(reads), path(index)

output:
tuple val(meta), path("*bam") , emit: bam
Expand Down