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Update sentieon bwamemindex #397

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merged 4 commits into from
Aug 8, 2023
Merged

Update sentieon bwamemindex #397

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c7828d8
Updating module for sentieon bwamem
asp8200 Aug 7, 2023
fd75f35
Setting output path using the prefix parameter
asp8200 Aug 7, 2023
afb19e7
Adding sentieon/bwaindex to modules.json
asp8200 Aug 8, 2023
4a24c69
Merge branch 'dev' into update_sentieon_bwamemindex
asp8200 Aug 8, 2023
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5 changes: 5 additions & 0 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -335,6 +335,11 @@
"git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
"installed_by": ["modules"]
},
"sentieon/bwaindex": {
"branch": "master",
"git_sha": "49af8ed458e28729e483bc96e5a57c28163b9ea0",
"installed_by": ["modules"]
},
"smncopynumbercaller": {
"branch": "master",
"git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
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30 changes: 20 additions & 10 deletions modules/local/sentieon/bwamemindex.nf → modules/nf-core/sentieon/bwaindex/main.nf
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41 changes: 41 additions & 0 deletions modules/nf-core/sentieon/bwaindex/meta.yml
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5 changes: 2 additions & 3 deletions subworkflows/local/prepare_references.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -17,8 +17,8 @@ include { GET_CHROM_SIZES } from '../../modul
include { SAMTOOLS_FAIDX as SAMTOOLS_EXTRACT_MT } from '../../modules/nf-core/samtools/faidx/main'
include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_GENOME } from '../../modules/nf-core/samtools/faidx/main'
include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT_SHIFT } from '../../modules/nf-core/samtools/faidx/main'
include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../modules/local/sentieon/bwamemindex'
include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../modules/local/sentieon/bwamemindex'
include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../modules/nf-core/sentieon/bwaindex/main'
include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../modules/nf-core/sentieon/bwaindex/main'
include { TABIX_BGZIPTABIX as TABIX_PBT } from '../../modules/nf-core/tabix/bgziptabix/main'
include { TABIX_TABIX as TABIX_DBSNP } from '../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_GNOMAD_AF } from '../../modules/nf-core/tabix/tabix/main'
Expand Down Expand Up @@ -144,4 +144,3 @@ workflow PREPARE_REFERENCES {
versions = ch_versions // channel: [ path(versions.yml) ]

}