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add masked_positions and masked_positions_file arguments to task polyphonia_detect_cross_contamination #499

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merged 5 commits into from
Dec 15, 2023
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add masked_positions and masked_positions_file arguments to task polyphonia_detect_cross_contamination #499

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34a9762
added masked-positions and masked-positions-file options
lakras Nov 23, 2023
82a6ced
corrected error in masked-positions-file command
lakras Nov 23, 2023
476f6f5
made masked positions file one file rather than an array
lakras Nov 23, 2023
7d8cafe
made masked-positions-file optional
lakras Dec 13, 2023
1539664
Merge branch 'master' into lk-polyphonia-masking
dpark01 Dec 13, 2023
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6 changes: 6 additions & 0 deletions pipes/WDL/tasks/tasks_intrahost.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,8 @@ task polyphonia_detect_cross_contamination {
Int min_read_depth = 100
Array[File]? read_depths
Int max_mismatches = 1
String? masked_positions
File? masked_positions_file

Array[File]? plate_maps
Int? plate_size = 96
Expand Down Expand Up @@ -44,6 +46,8 @@ task polyphonia_detect_cross_contamination {
read_depths: { description: "Read depth tables (tab-separated, no header: reference name, position, read depth); provide alongside vcf files or heterozygosity tables if min-depth>0" }
min_genome_coverage: { description: "Minimum proportion genome covered for a sample to be included" }
max_mismatches: { description: "Maximum allowed bases in contaminating sample consensus not matching contaminated sample alleles" }
masked_positions: { description: "1-indexed positions to mask (e.g., 1-10,50,55-70)" }
masked_positions_file: { description: "1-indexed positions to mask, one per line" }

plate_maps: { description: "Optional plate map(s) (tab-separated, no header: sample name, plate position (e.g., A8))" }
plate_size: { description: "Standard plate size (6-well, 12-well, 24, 48, 96, 384, 1536, 3456)" }
Expand Down Expand Up @@ -83,6 +87,8 @@ task polyphonia_detect_cross_contamination {
~{'--min-readcount ' + min_readcount} \
~{'--max-mismatches ' + max_mismatches} \
~{'--min-maf ' + min_maf} \
~{'--masked-positions ' + masked_positions} \
--masked-positions-file ~{masked_positions_file} \
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If masked positions file is optional, you should use the same optional parameter syntax as masked positions so it works properly if empty

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Updated, thank you!

$PLATE_MAPS_INPUT \
~{'--plate-size ' + plate_size} \
~{'--plate-columns ' + plate_columns} \
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