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Dev #69

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merged 3 commits into from
Aug 1, 2023
Merged

Dev #69

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e2deaa1
updated config for threshold report with subsample
ssnn-airr Jul 26, 2023
feedb3f
updated path for enchantr 0.1.4
ssnn-airr Aug 1, 2023
6e9a890
Merge branch 'dev' into dev
ggabernet Aug 1, 2023
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2 changes: 1 addition & 1 deletion conf/modules.config
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Expand Up @@ -442,7 +442,7 @@ process {
'findthreshold_edge':0.9,
'findthreshold_cutoff':'user',
'findthreshold_spc':0.995,
'subsample':8000]
'subsample':10000]
}

withName: DEFINE_CLONES_COMPUTE {
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6 changes: 3 additions & 3 deletions docs/output.md
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Expand Up @@ -388,10 +388,10 @@ This folder is genereated when `detect_contamination` is set to `true`.

- `clonal_analysis/find_threshold/`
- `*log`: Log of the process that will be parsed to generate a report.
- `all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the
Junction regions as determined by Shazam.
- `all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples.
- `all_reps_dist_report`: Report
- `tables/all_reps_threshold-mean.tsv`: Mean of all hamming distance thresholds of the
Junction regions as determined by Shazam.
- `tables/all_reps_threshold-summary.tsv`: Thresholds for each group of `--cloneby` samples.

</details>

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4 changes: 2 additions & 2 deletions modules/local/enchantr/find_threshold.nf
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Expand Up @@ -36,8 +36,8 @@ process FIND_THRESHOLD {
// tuple val(meta), path("*threshold-pass.tsv"), emit: tab // sequence tsv in AIRR format
path("*_command_log.txt"), emit: logs //process logs
path "*_report"
path "*_threshold-summary.tsv", emit: threshold_summary
path "*_threshold-mean.tsv", emit: mean_threshold
path "all_reps_dist_report/tables/*_threshold-summary.tsv", emit: threshold_summary
path "all_reps_dist_report/tables/*_threshold-mean.tsv", emit: mean_threshold
path "versions.yml", emit: versions

script:
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