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merge samples across lanes in demux deplete #369

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merge samples across lanes in demux deplete #369

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40def8e
WIP merge bams by sample in demux_deplete
tomkinsc Aug 31, 2021
c161a21
include ".merged" suffix in merged output basename
tomkinsc Aug 31, 2021
e1fd649
Merge branch 'master' into ct-demux-deplete-merge-lanes
tomkinsc Sep 28, 2021
2e6c8a9
s/meta_by_sample/meta_sample/ in demux_deplete
tomkinsc Sep 28, 2021
6230564
Merge branch 'master' into ct-demux-deplete-merge-lanes
tomkinsc Sep 28, 2021
45cec20
Merge branch 'master' into ct-demux-deplete-merge-lanes
tomkinsc Nov 3, 2023
e4c0321
Merge branch 'master' into ct-demux-deplete-merge-lanes
tomkinsc Jan 5, 2024
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22 changes: 22 additions & 0 deletions pipes/WDL/workflows/demux_deplete.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,7 @@ import "../tasks/tasks_demux.wdl" as demux
import "../tasks/tasks_taxon_filter.wdl" as taxon_filter
import "../tasks/tasks_reports.wdl" as reports
import "../tasks/tasks_ncbi.wdl" as ncbi
import "../tasks/tasks_read_utils.wdl" as read_utils

workflow demux_deplete {
meta {
Expand Down Expand Up @@ -138,6 +139,7 @@ workflow demux_deplete {
sub_keys = default_filename_keys
}
}

call demux.merge_maps as meta_sample {
input: maps_jsons = meta_default_sample.out_json
}
Expand Down Expand Up @@ -167,6 +169,13 @@ workflow demux_deplete {
}
}

call read_utils.group_bams_by_sample as grouped_passing {
input:
bam_filepaths = select_all(cleaned_bam_passing)
}

#scatter(name_reads in zip(group_bams_by_sample.sample_names, group_bams_by_sample.grouped_bam_filepaths)) {

#### SRA submission prep
if(defined(biosample_map)) {
call ncbi.sra_meta_prep {
Expand Down Expand Up @@ -199,6 +208,18 @@ workflow demux_deplete {
counts_txt = spikein.report
}

scatter(name_reads in zip(grouped_passing.sample_names, grouped_passing.grouped_bam_filepaths)) {
Boolean ampseq = (meta_sample.merged[name_reads.left]["amplicon_set"] != "")
String orig_name = meta_sample.merged[name_reads.left]["sample_original"]

call read_utils.merge_and_reheader_bams {
input:
in_bams = name_reads.right,
sample_name = orig_name,
out_basename = "${orig_name}.merged"
}
}

# TO DO: flag all libraries where highest spike-in is not what was expected in extended samplesheet

output {
Expand All @@ -211,6 +232,7 @@ workflow demux_deplete {
File meta_by_sample_json = meta_sample.merged_json

Array[File] cleaned_reads_unaligned_bams = select_all(cleaned_bam_passing)
Array[File] cleaned_reads_unaligned_merged_bams = select_all(merge_and_reheader_bams.out_bam)
Array[File] cleaned_bams_tiny = select_all(empty_bam)
Array[Int] read_counts_depleted = deplete.depletion_read_count_post

Expand Down
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