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ramprasadnramprasadn
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Merge branch 'dev' into removeredundantprocess
2 parents 4eb38b0 + efbdf46 commit 2001331

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Lines changed: 693 additions & 675 deletions

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‎CHANGELOG.md‎

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@@ -10,6 +10,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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### `Changed`
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- Remove redundant indexing processes by enabling native index creation: use `--CREATE_INDEX true` in Picard MarkDuplicates, `--write-index=tbi` in bcftools tools (`SPLIT_MULTIALLELICS_MT`, `REMOVE_DUPLICATES_MT`, `BCFTOOLS_MERGE_MT`, `BCFTOOLS_ANNOTATE`, `BCFTOOLS_REHEADER`, `BCFTOOLS_SORT_ME`) and SVDB_MERGE; eliminate downstream `SAMTOOLS_INDEX` and `TABIX_TABIX` steps across `align_bwa_bwamem2_bwameme`, `postprocess_MT_calls`, `call_mobile_elements`, `call_structural_variants`, and `variant_evaluation` subworkflows [#859](https://github.com/nf-core/raredisease/pull/859)
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- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for annotate_rhocallviz and annotate_genome_snvs subworkflows [#858](https://github.com/nf-core/raredisease/pull/858)
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- Expand annotate_rhocallviz test with snapshot assertions [#858](https://github.com/nf-core/raredisease/pull/858)
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- Refactor scatter_genome subworkflow: alias GAWK as `GENOME_FAI_TO_BED`, remove `val_save_reference` parameter, move interval flattening into `annotate_genome_snvs` [#857](https://github.com/nf-core/raredisease/pull/857)
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- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for qc_bam subworkflow [#853](https://github.com/nf-core/raredisease/pull/853)
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- Replace `ch_publish`/`subworkflow_results` with named typed channel emits for alignment and subsample-MT subworkflows [#850](https://github.com/nf-core/raredisease/pull/850)

‎main.nf‎

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@@ -566,6 +566,14 @@ workflow NFCORE_RAREDISEASE {
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qc_bam_verifybamid_ud = RAREDISEASE.out.qc_bam_verifybamid_ud // channel: [ val(meta), path(ud) ]
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qc_bam_wgsmetrics_wg = RAREDISEASE.out.qc_bam_wgsmetrics_wg // channel: [ val(meta), path(metrics) ]
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qc_bam_wgsmetrics_y = RAREDISEASE.out.qc_bam_wgsmetrics_y // channel: [ val(meta), path(metrics) ]
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annotate_genome_snvs_bcftools_concat_tbi = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi // channel: [ val(meta), path(tbi) ]
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annotate_genome_snvs_bcftools_concat_vcf = RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf // channel: [ val(meta), path(vcf) ]
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annotate_genome_snvs_chromograph_autozyg_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots // channel: [ val(meta), path(png) ]
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annotate_genome_snvs_chromograph_regions_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_regions_plots // channel: [ val(meta), path(png) ]
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annotate_genome_snvs_chromograph_sites_plots = RAREDISEASE.out.annotate_genome_snvs_chromograph_sites_plots // channel: [ val(meta), path(png) ]
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annotate_genome_snvs_rhocall_viz_bed = RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_bed // channel: [ val(meta), path(bed) ]
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annotate_genome_snvs_rhocall_viz_wig = RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_wig // channel: [ val(meta), path(wig) ]
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annotate_genome_snvs_ucsc_wigtobigwig_bw = RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ]
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subsample_mt_bai = RAREDISEASE.out.subsample_mt_bai // channel: [ val(meta), path(bai) ]
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subsample_mt_bam = RAREDISEASE.out.subsample_mt_bam // channel: [ val(meta), path(bam) ]
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publish = RAREDISEASE.out.publish
@@ -722,45 +730,53 @@ workflow {
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)
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publish:
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alignment = NFCORE_RAREDISEASE.out.align_genome_marked_bam
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.mix(NFCORE_RAREDISEASE.out.align_genome_marked_bai)
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.mix(NFCORE_RAREDISEASE.out.align_genome_marked_cram)
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.mix(NFCORE_RAREDISEASE.out.align_genome_marked_crai)
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.mix(NFCORE_RAREDISEASE.out.align_markdup_metrics)
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.mix(NFCORE_RAREDISEASE.out.subsample_mt_bam)
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.mix(NFCORE_RAREDISEASE.out.subsample_mt_bai)
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fastp = NFCORE_RAREDISEASE.out.align_fastp_out
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ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv
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qc_bam = NFCORE_RAREDISEASE.out.qc_bam_chromograph_cov_plots.transpose()
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_d4)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_txt)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_summary_txt)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics.transpose())
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.mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf.transpose())
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.mix(NFCORE_RAREDISEASE.out.qc_bam_sambamba_depth_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_cov)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_wig)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ancestry)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_log)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_mu)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_self_sm)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y)
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processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals
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subworkflow_results = NFCORE_RAREDISEASE.out.publish
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alignment = NFCORE_RAREDISEASE.out.align_genome_marked_bam
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.mix(NFCORE_RAREDISEASE.out.align_genome_marked_bai)
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.mix(NFCORE_RAREDISEASE.out.align_genome_marked_cram)
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.mix(NFCORE_RAREDISEASE.out.align_genome_marked_crai)
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.mix(NFCORE_RAREDISEASE.out.align_markdup_metrics)
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.mix(NFCORE_RAREDISEASE.out.subsample_mt_bam)
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.mix(NFCORE_RAREDISEASE.out.subsample_mt_bai)
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fastp = NFCORE_RAREDISEASE.out.align_fastp_out
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ngsbits_samplegender = NFCORE_RAREDISEASE.out.qc_bam_ngsbits_samplegender_tsv
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qc_bam = NFCORE_RAREDISEASE.out.qc_bam_chromograph_cov_plots.transpose()
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_global_txt)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_per_base_d4)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_quantized_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_regions_txt)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_summary_txt)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_mosdepth_thresholds_csi)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collecthsmetrics_metrics)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_metrics.transpose())
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.mix(NFCORE_RAREDISEASE.out.qc_bam_picard_collectmultiplemetrics_pdf.transpose())
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.mix(NFCORE_RAREDISEASE.out.qc_bam_sambamba_depth_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_cov)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_tiddit_cov_wig)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_ucsc_wigtobigwig_bw)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ancestry)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_bed)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_log)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_mu)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_self_sm)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_verifybamid_ud)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_wg)
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.mix(NFCORE_RAREDISEASE.out.qc_bam_wgsmetrics_y)
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annotate_snv_genome = NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_vcf
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.mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_bcftools_concat_tbi)
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.mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_autozyg_plots)
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.mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_regions_plots)
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.mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_chromograph_sites_plots)
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.mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_bed)
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.mix(NFCORE_RAREDISEASE.out.annotate_genome_snvs_rhocall_viz_wig)
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annotate_snv_genome_rhocallviz_bw = NFCORE_RAREDISEASE.out.annotate_genome_snvs_ucsc_wigtobigwig_bw
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processed_references = NFCORE_RAREDISEASE.out.scatter_genome_split_intervals
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subworkflow_results = NFCORE_RAREDISEASE.out.publish
764780
}
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766782
output {
@@ -776,6 +792,12 @@ output {
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qc_bam {
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path { _meta, _file -> "qc_bam/" }
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}
795+
annotate_snv_genome {
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path { _meta, _file -> "annotate_snv/genome/" }
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}
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annotate_snv_genome_rhocallviz_bw {
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path { meta, _file -> "annotate_snv/genome/${meta.sample}_rhocallviz/" }
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}
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processed_references {
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path { _meta, _file -> "processed_references/" }
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enabled params.save_reference

‎subworkflows/local/annotate_genome_snvs/main.nf‎

Lines changed: 15 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -41,10 +41,11 @@ workflow ANNOTATE_GENOME_SNVS {
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val_vep_cache_version // string: vep version ex: 107
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main:
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ch_cadd_vcf = channel.empty()
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ch_vcf_scatter_in = channel.empty()
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ch_vep_in = channel.empty()
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ch_chromograph_publish = channel.empty()
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ch_cadd_vcf = channel.empty()
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ch_chromograph_regions_plots = channel.empty()
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ch_chromograph_sites_plots = channel.empty()
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ch_vcf_scatter_in = channel.empty()
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ch_vep_in = channel.empty()
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ch_vcf
5051
.filter { meta, _vcf, _tbi ->
@@ -186,8 +187,8 @@ workflow ANNOTATE_GENOME_SNVS {
186187
UPD_REGIONS(ch_upd_in)
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CHROMOGRAPH_SITES([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_SITES.out.bed)
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CHROMOGRAPH_REGIONS([[],[]], [[],[]], [[],[]], [[],[]], [[],[]], UPD_REGIONS.out.bed, [[],[]])
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ch_chromograph_publish = CHROMOGRAPH_SITES.out.plots
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.mix(CHROMOGRAPH_REGIONS.out.plots)
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ch_chromograph_sites_plots = CHROMOGRAPH_SITES.out.plots
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ch_chromograph_regions_plots = CHROMOGRAPH_REGIONS.out.plots
191192
}
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193194
BCFTOOLS_CONCAT.out.vcf
@@ -202,14 +203,13 @@ workflow ANNOTATE_GENOME_SNVS {
202203
//rhocall_viz
203204
ANNOTATE_RHOCALLVIZ(ch_genome_chrsizes, ch_samples, ch_vep_ann_index )
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205-
ch_publish = ch_chromograph_publish
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.mix(ch_concat_vcf_out)
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.mix(ch_concat_tbi_out)
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.map { meta, value -> ['annotate_snv/genome/', [meta, value]] }
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.mix(ANNOTATE_RHOCALLVIZ.out.publish)
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emit:
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tbi = ch_concat_tbi_out // channel: [ val(meta), path(tbi) ]
213-
vcf_ann = ch_concat_vcf_out // channel: [ val(meta), path(vcf) ]
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publish = ch_publish // channel: [ val(destination), val(value) ]
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bcftools_concat_tbi = ch_concat_tbi_out // channel: [ val(meta), path(tbi) ]
208+
bcftools_concat_vcf = ch_concat_vcf_out // channel: [ val(meta), path(vcf) ]
209+
chromograph_autozyg_plots = ANNOTATE_RHOCALLVIZ.out.chromograph_autozyg_plots // channel: [ val(meta), path(png) ]
210+
chromograph_regions_plots = ch_chromograph_regions_plots // channel: [ val(meta), path(png) ]
211+
chromograph_sites_plots = ch_chromograph_sites_plots // channel: [ val(meta), path(png) ]
212+
rhocall_viz_bed = ANNOTATE_RHOCALLVIZ.out.rhocall_viz_bed // channel: [ val(meta), path(bed) ]
213+
rhocall_viz_wig = ANNOTATE_RHOCALLVIZ.out.rhocall_viz_wig // channel: [ val(meta), path(wig) ]
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ucsc_wigtobigwig_bw = ANNOTATE_RHOCALLVIZ.out.ucsc_wigtobigwig_bw // channel: [ val(meta), path(bw) ]
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}

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