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Update somatic vc subworkflow sage and manta #35

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RaqManzano wants to merge 3 commits into from
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Update somatic vc subworkflow sage and manta #35

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82360de
Update somatic vc subworkflow sage and manta
RaqManzano Jul 23, 2024
3e05ea9
prettier, eclint and manta fix
RaqManzano Jul 23, 2024
923e897
fix typo
RaqManzano Jul 23, 2024
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6 changes: 3 additions & 3 deletions subworkflows/local/bam_variant_calling_somatic_manta/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@ include { MANTA_SOMATIC } from '../../../modules/nf-core/manta/somatic/main'
workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
take:
cram // channel: [mandatory] [ meta, cram1, crai1, cram2, crai2 ]
fasta // channel: [mandatory] [ fasta ]
fasta_fai // channel: [mandatory] [ fasta_fai ]
fasta // channel: [mandatory] [ meta, fasta ]
fasta_fai // channel: [mandatory] [ meta, fasta_fai ]
intervals // channel: [mandatory] [ interval.bed.gz, interval.bed.gz.tbi ] or [ [], [] ] if no intervals

main:
Expand All @@ -24,7 +24,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_MANTA {
[it[0], it[1], it[2], it[3], it[4], bed_gz, bed_tbi]
}

MANTA_SOMATIC(cram_intervals, fasta, fasta_fai)
MANTA_SOMATIC(cram_intervals, fasta, fasta_fai, [])

candidate_small_indels_vcf = MANTA_SOMATIC.out.candidate_small_indels_vcf
candidate_small_indels_vcf_tbi = MANTA_SOMATIC.out.candidate_small_indels_vcf_tbi
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11 changes: 8 additions & 3 deletions subworkflows/local/bam_variant_calling_somatic_sage/main.nf
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Expand Up @@ -43,12 +43,17 @@ workflow BAM_VARIANT_CALLING_SOMATIC_SAGE {
cram_intervals = cram.combine(intervals)
// Move num_intervals to meta map and reorganize channel for SAGE module
.map{ meta, cram1, crai1, cram2, crai2, intervals, num_intervals -> [ meta + [ num_intervals:num_intervals ], cram1, crai1, cram2, crai2, intervals ]}

// init resources
sage_highconfidence = params.sage_highconfidence ? Channel.fromPath(params.sage_highconfidence).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([])
sage_actionablepanel = params.sage_actionablepanel ? Channel.fromPath(params.sage_actionablepanel).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([])
sage_knownhotspots = params.sage_knownhotspots ? Channel.fromPath(params.sage_knownhotspots).collect().map{ it -> [ [ id:it[0].baseName ], it ] } : Channel.value([])
SAGE(
cram_intervals,
sage_ensembl,
Channel.fromPath(params.sage_highconfidence).collect().map{ it -> [ [ id:it[0].baseName ], it ] },
Channel.fromPath(params.sage_actionablepanel).collect().map{ it -> [ [ id:it[0].baseName ], it ] },
Channel.fromPath(params.sage_knownhotspots).collect().map{ it -> [ [ id:it[0].baseName ], it ] },
sage_highconfidence,
sage_actionablepanel,
sage_knownhotspots,
fasta,
fasta_fai,
dict)
Expand Down