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Remove CONVERT_ONT_READNAMES #237

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merged 2 commits into from
Jul 1, 2024
Merged

Remove CONVERT_ONT_READNAMES #237

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1c6fd2c
Remove CONVERT_ONT_READNAMES
fellen31 Jun 28, 2024
5242797
Merge branch 'dev' into remove-convert-ont-readnames
fellen31 Jul 1, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -20,6 +20,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Removed`

- [#237](https://github.com/genomic-medicine-sweden/nallo/pull/237) - Removed the CONVERT_ONT_READNAMES module that was run before calling repeats with TRGT
- [#238](https://github.com/genomic-medicine-sweden/nallo/pull/238) - Removed the `--extra_gvcfs` parameter

### `Fixed`
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68 changes: 0 additions & 68 deletions modules/local/convert_ont_read_names.nf
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This file was deleted.

16 changes: 2 additions & 14 deletions workflows/nallo.nf
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Expand Up @@ -29,7 +29,6 @@ include { SNV_ANNOTATION } from '../subworkflows/local/snv_annotatio

// local
include { FQCRS } from '../modules/local/fqcrs'
include { CONVERT_ONT_READ_NAMES } from '../modules/local/convert_ont_read_names'
include { BUILD_INTERVALS } from '../modules/local/build_intervals/main'
include { SPLIT_BED_CHUNKS } from '../modules/local/split_bed_chunks/main'
include { SAMTOOLS_MERGE } from '../modules/nf-core/samtools/merge/main'
Expand Down Expand Up @@ -318,19 +317,8 @@ workflow NALLO {
}

if(!params.skip_repeat_wf) {
// Repeat analysis with TRGT

// Hack read names
if (params.preset == "ONT_R10") {
CONVERT_ONT_READ_NAMES(hap_bam_bai)
ch_versions = ch_versions.mix(CONVERT_ONT_READ_NAMES.out.versions)

ch_repeat_analysis_in = CONVERT_ONT_READ_NAMES.out.bam_bai
} else {
ch_repeat_analysis_in = hap_bam_bai
}

REPEAT_ANALYSIS( ch_repeat_analysis_in, fasta, fai, ch_trgt_bed )
// Call repeats with TRGT
REPEAT_ANALYSIS( hap_bam_bai, fasta, fai, ch_trgt_bed )
ch_versions = ch_versions.mix(REPEAT_ANALYSIS.out.versions)
}
}
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