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[TheiaCov] wfs add percentage_mapped_reads #641

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Nov 4, 2024
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c64b57b
Added percentage_mapped_reads output to ivar_consensus.wdl and update…
fraser-combe Sep 9, 2024
93e2d89
update mapped reads trying read_float
fraser-combe Sep 10, 2024
5298eff
get read numbers from stats file
fraser-combe Sep 10, 2024
85a8cc8
get read numbers from stats filev2
fraser-combe Sep 10, 2024
9c2cb18
change from bc to awk for calculation
fraser-combe Sep 10, 2024
c57edc4
update awk
fraser-combe Sep 10, 2024
76b62ce
metric output txt instead of csv
fraser-combe Sep 10, 2024
e6afcdd
reswitchack to read_string output t
fraser-combe Sep 10, 2024
dba965b
percentage mapped reads based on trimmed bam file theiacov_ont
fraser-combe Sep 16, 2024
dd7b3e7
update theiacov-ont for mapped reads
fraser-combe Sep 17, 2024
b803c7a
Merge remote-tracking branch 'origin/main' into fc-theiacov-mapped-re…
fraser-combe Oct 2, 2024
f6d5393
pass output ivar cons mapped reads to wf for terra output
fraser-combe Oct 2, 2024
f888c65
perc mapped reads output flu track PE, ONT and clearlabs and doc update
fraser-combe Oct 3, 2024
92733ea
updated namings outputs cov_ONT and removed extra call assembly metrics
fraser-combe Oct 3, 2024
72db285
change naming output stat n coverage task
fraser-combe Oct 3, 2024
69b4666
update flu mapped reads perc variable name
fraser-combe Oct 3, 2024
b9320d7
make theiacov_ont conditional output flu mapped reads
fraser-combe Oct 3, 2024
0aeb272
wdl does not support if cond in output change to select first
fraser-combe Oct 3, 2024
4846b1e
wdl does not support if cond in output change to select first
fraser-combe Oct 3, 2024
33ab026
combine flu and non flu into same mapped reads output
fraser-combe Oct 3, 2024
7070c62
correct assembled reads call
fraser-combe Oct 21, 2024
e23b19a
update mdsums
fraser-combe Oct 21, 2024
b790973
update clearlabs for statncov call
fraser-combe Oct 21, 2024
58ac2ee
float?
fraser-combe Oct 21, 2024
45568de
mdsums and pe wf update flu irma defined
fraser-combe Oct 21, 2024
5454111
mdsum pe
fraser-combe Oct 21, 2024
6493640
move to flue track
fraser-combe Oct 22, 2024
56a4a30
tidy output pe and ont
fraser-combe Oct 22, 2024
108612b
update strings and provide default values
fraser-combe Oct 24, 2024
842691a
clean tab/spaces echo
fraser-combe Oct 31, 2024
cd32e74
my fav commit mdsums!
fraser-combe Oct 31, 2024
f3b316f
remove extra space because it was bothering me
sage-wright Nov 4, 2024
979d636
adding a space because i am crazy
sage-wright Nov 4, 2024
25a2da2
update flu output
fraser-combe Nov 4, 2024
23ead27
update outputs
fraser-combe Nov 4, 2024
8b8aea1
remove string in name
fraser-combe Nov 4, 2024
1b58829
correctly name percentage mapped reads
fraser-combe Nov 4, 2024
85cc203
correct output in flu track wdl
fraser-combe Nov 4, 2024
5c5cc4f
update mdsums
fraser-combe Nov 4, 2024
1888803
primtrim output
fraser-combe Nov 4, 2024
e81d7b9
another mdsum
fraser-combe Nov 4, 2024
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update outputs
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fraser-combe committed Nov 4, 2024
commit 23ead27b7a30a2150e64468a6c3d68e422ef6569
2 changes: 1 addition & 1 deletion workflows/theiacov/wf_theiacov_illumina_pe.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -440,6 +440,6 @@ workflow theiacov_illumina_pe {
String? qc_check = qc_check_task.qc_check
File? qc_standard = qc_check_task.qc_standard
# Capture percentage_mapped_reads from ivar_consensus task or flu_track task
String percentage_mapped_reads = select_first([ivar_consensus.percentage_mapped_reads, flu_track.percentage_mapped_reads,""])
String percentage_mapped_reads = select_first([ivar_consensus.percentage_mapped_reads, flu_track.percentage_mapped_reads, ""])
}
}
2 changes: 1 addition & 1 deletion workflows/theiacov/wf_theiacov_ont.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -428,6 +428,6 @@ workflow theiacov_ont {
String? qc_check = qc_check_task.qc_check
File? qc_standard = qc_check_task.qc_standard
# Non-flu specific outputs
String percentage_mapped_reads = select_first([flu_track.percentage_mapped_reads, stats_n_coverage.percentage_mapped_reads,""])
String percentage_mapped_reads = select_first([stats_n_coverage.percentage_mapped_reads, flu_track.ha_na_mapped_reads_percentage_string, ""])
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}
}
2 changes: 1 addition & 1 deletion workflows/utilities/wf_flu_track.wdl
Original file line number Diff line number Diff line change
Expand Up @@ -260,7 +260,7 @@ workflow flu_track {
File? irma_na_bam = irma.seg_na_bam
String ha_na_assembly_coverage = ha_na_assembly_coverage_string
# calulate mapped reads percentage for flu samples
String percentage_mapped_reads = flu_stats_n_coverage.percentage_mapped_reads
String percentage_mapped_reads = ha_na_mapped_reads_percentage_string
# GenoFLU outputs
String? genoflu_version = genoflu.genoflu_version
String? genoflu_genotype = genoflu.genoflu_genotype
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