Include lofreq module, and merge lofreq and ivar results #432
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add lofreq module and subworkflow 'LOFREQ_IVAR'
Joon-Klaps
requested changes
Jun 13, 2024
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename } | ||
| ] | ||
| } | ||
| withName: 'VARIANTS_IVAR:IVAR_VARIANTS' { |
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| withName: 'VARIANTS_IVAR:IVAR_VARIANTS' { | |
| withName: 'IVAR_VARIANTS' { |
| @@ -6,7 +6,7 @@ | |||
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| def valid_params = [ | |||
| protocols : ['metagenomic', 'amplicon'], | |||
| variant_callers : ['ivar', 'bcftools'], | |||
| variant_callers : ['ivar', 'bcftools'. 'lofreq'], | |||
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update parameter schema nf-core schema build as wel
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| include { LOFREQ_CALLPARALLEL } from '../modules/nf-core/lofreq/callparallel/main' | ||
| include { BCFTOOLS_MERGE } from '../modules/nf-core/bcftools/merge/main' | ||
| include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' |
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| include { LOFREQ_CALLPARALLEL } from '../modules/nf-core/lofreq/callparallel/main' | |
| include { BCFTOOLS_MERGE } from '../modules/nf-core/bcftools/merge/main' | |
| include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' | |
| include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' |
No need to call modules in the main workflow if they are not used in that workflow. You already call them in the LOFREQ_IVAR subworkflow.
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| // SUBWORKFLOW: Call variants with Lofreq | ||
| ch_lofreq_vcf = Channel.empty() | ||
| //ch_vcf = Channel.empty() | ||
| //ch_lofreq_tbi = Channel.empty() | ||
| ch_bam | ||
| .join(ch_bai, by: [0]) | ||
| .map{ meta,bam,bai -> [meta, bam, bai, []] } | ||
| .set{ ch_lofreq_bam_bai } | ||
| if (!params.skip_variants && variant_caller == 'lofreq') { | ||
| LOFREQ_CALLPARALLEL ( | ||
| ch_lofreq_bam_bai, | ||
| PREPARE_GENOME.out.fasta, | ||
| PREPARE_GENOME.out.fai | ||
| ) | ||
| ch_lofreq_vcf = LOFREQ_CALLPARALLEL.out.vcf | ||
| //ch_lofreq_tbi = LOFREQ_CALLPARALLEL.out.tbi | ||
| ch_versions = ch_versions.mix(LOFREQ_CALLPARALLEL.out.versions) | ||
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| // SUBWORKFLOW: Call variants with ivar | ||
| VARIANTS_IVAR ( | ||
| ch_bam, | ||
| PREPARE_GENOME.out.fasta, | ||
| (params.protocol == 'amplicon' || !params.skip_asciigenome || !params.skip_markduplicates) ? PREPARE_GENOME.out.fai : [], | ||
| (params.protocol == 'amplicon' || !params.skip_asciigenome || !params.skip_markduplicates) ? PREPARE_GENOME.out.chrom_sizes : [], | ||
| params.gff ? PREPARE_GENOME.out.gff : [], | ||
| (params.protocol == 'amplicon' && params.primer_bed) ? PREPARE_GENOME.out.primer_bed : [], | ||
| PREPARE_GENOME.out.snpeff_db, | ||
| PREPARE_GENOME.out.snpeff_config, | ||
| ch_ivar_variants_header_mqc | ||
| ) | ||
| ch_vcf = VARIANTS_IVAR.out.vcf | ||
| ch_tbi = VARIANTS_IVAR.out.tbi | ||
| ch_ivar_counts_multiqc = VARIANTS_IVAR.out.multiqc_tsv | ||
| ch_bcftools_stats_multiqc = VARIANTS_IVAR.out.stats | ||
| ch_snpeff_multiqc = VARIANTS_IVAR.out.snpeff_csv | ||
| ch_snpsift_txt = VARIANTS_IVAR.out.snpsift_txt | ||
| ch_versions = ch_versions.mix(VARIANTS_IVAR.out.versions) | ||
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| // MODULE: Merge ivar and lofreq variants | ||
| BCFTOOLS_MERGE( | ||
| ch_lofreq_vcf, | ||
| ch_vcf, | ||
| //ch_vcf, | ||
| //ch_tbi, | ||
| PREPARE_GENOME.out.fasta, | ||
| PREPARE_GENOME.out.fai | ||
| ) | ||
| ch_merged_vcf = BCFTOOLS_MERGE.out.merged_variants | ||
| ch_versions = ch_versions.mix(BCFTOOLS_MERGE.out.versions) | ||
| } | ||
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Think you forgot to refactor this by calling the subworkflow
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| lofreq_bam // channel: [ val(meta), [ bam ], [ bai ] ] | ||
| bam // channel: [ val(meta), [ bam ] ] // for ivar | ||
| fasta // channel: /path/to/genome.fasta | ||
| fai // channel: /path/to/genome.fai | ||
| sizes // channel: /path/to/genome.sizes | ||
| gff // channel: /path/to/genome.gff | ||
| bed // channel: /path/to/primers.bed | ||
| snpeff_db // channel: /path/to/snpeff_db/ | ||
| snpeff_config // channel: /path/to/snpeff.config | ||
| ivar_multiqc_header // channel: /path/to/multiqc_header for ivar variants | ||
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