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adds channels to meme mt align #582

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merged 1 commit into from
Jul 4, 2024
Merged

adds channels to meme mt align #582

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8 changes: 6 additions & 2 deletions subworkflows/local/align.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -100,7 +100,9 @@ workflow ALIGN {
ch_genome_bwamemeindex,
ch_genome_fasta,
ch_genome_dictionary,
ch_genome_fai
ch_genome_fai,
val_mbuffer_mem,
val_sort_threads
)

ALIGN_MT_SHIFT (
Expand All @@ -111,7 +113,9 @@ workflow ALIGN {
ch_mtshift_bwamemeindex,
ch_mtshift_fasta,
ch_mtshift_dictionary,
ch_mtshift_fai
ch_mtshift_fai,
val_mbuffer_mem,
val_sort_threads
)

ch_mt_marked_bam = ALIGN_MT.out.marked_bam
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20 changes: 11 additions & 9 deletions subworkflows/local/alignment/align_MT.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,14 +14,16 @@ include { SAMTOOLS_SORT as SAMTOOLS_SORT_MT } fr

workflow ALIGN_MT {
take:
ch_fastq // channel: [mandatory] [ val(meta), [ path(reads) ] ]
ch_ubam // channel: [mandatory] [ val(meta), path(bam) ]
ch_bwaindex // channel: [mandatory for sentieon] [ val(meta), path(index) ]
ch_bwamem2index // channel: [mandatory for bwamem2] [ val(meta), path(index) ]
ch_bwamemeindex // channel: [mandatory for bwameme] [ val(meta), path(index) ]
ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_dict // channel: [mandatory] [ val(meta), path(dict) ]
ch_fai // channel: [mandatory] [ val(meta), path(fai) ]
ch_fastq // channel: [mandatory] [ val(meta), [ path(reads) ] ]
ch_ubam // channel: [mandatory] [ val(meta), path(bam) ]
ch_bwaindex // channel: [mandatory for sentieon] [ val(meta), path(index) ]
ch_bwamem2index // channel: [mandatory for bwamem2] [ val(meta), path(index) ]
ch_bwamemeindex // channel: [mandatory for bwameme] [ val(meta), path(index) ]
ch_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_dict // channel: [mandatory] [ val(meta), path(dict) ]
ch_fai // channel: [mandatory] [ val(meta), path(fai) ]
val_mbuffer_mem // integer: [mandatory] default: 3072
val_sort_threads // integer: [mandatory] default: 4

main:
ch_versions = Channel.empty()
Expand All @@ -39,7 +41,7 @@ workflow ALIGN_MT {
ch_align = BWA_MEM_MT.out.bam
ch_versions = ch_versions.mix(BWA_MEM_MT.out.versions.first())
} else if (params.aligner.equals("bwameme")) {
BWAMEME_MEM_MT (ch_fastq, ch_bwamemeindex, ch_fasta, true)
BWAMEME_MEM_MT (ch_fastq, ch_bwamemeindex, ch_fasta, true, val_mbuffer_mem, val_sort_threads)
ch_align = BWAMEME_MEM_MT.out.bam
ch_versions = ch_versions.mix(BWAMEME_MEM_MT.out.versions.first())
}
Expand Down