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Update 20240402 #313

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merged 3 commits into from
Apr 2, 2024
Merged

Update 20240402 #313

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f66bc84
Update to v3.13.20240402
erinyoung Apr 2, 2024
5f5c438
Added maintenance schedule
erinyoung Apr 2, 2024
f5700eb
Update freyja to 1.5.0-04_02_2024-00-47-2024-04-02
erinyoung Apr 2, 2024
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2 changes: 2 additions & 0 deletions README.md
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Expand Up @@ -266,6 +266,8 @@ Pangolin, Nextclade, and any analysis that evaluates the consensus fasta are not
nextflow pull UPHL-BioNGS/Cecret
```

Cecret has a weekly update schedule. Cecret's versions have three numbers : X.Y.Z. If the first number, X, changes, there has been a major modification. Params may have changed or subworkflows/channels may have been modified. If the second number, Y, changes, there has been a minor to moderate change. These are mainly for bug fixes or the changing the defaults of params. If the last number has been modified, Z, the workflow is basically the same, there have just been some updates in the containers pulled for the workflow. Most of these updates are to keep Freyja, NextClade, and Pangolin current for SARS-CoV-2 analysis.

## Quality Assessment
The quality of a sequencing run is very important. As such, many values are recorded so that the **End User** can assess the quality of the results produced from a sequencing run.

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6 changes: 3 additions & 3 deletions modules/freyja.nf
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Expand Up @@ -3,7 +3,7 @@ process freyja_variants {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/freyja:1.5.0-03_25_2024-00-45-2024-03-26'
container 'staphb/freyja:1.5.0-04_02_2024-00-47-2024-04-02'

//#UPHLICA maxForks 10
//#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge'
Expand Down Expand Up @@ -53,7 +53,7 @@ process freyja_demix {
label "process_medium"
//errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/freyja:1.5.0-03_25_2024-00-45-2024-03-26'
container 'staphb/freyja:1.5.0-04_02_2024-00-47-2024-04-02'


//#UPHLICA maxForks 10
Expand Down Expand Up @@ -105,7 +105,7 @@ process freyja_aggregate {
tag "Aggregating results from freyja"
label "process_single"
publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/freyja:1.5.0-03_25_2024-00-45-2024-03-26'
container 'staphb/freyja:1.5.0-04_02_2024-00-47-2024-04-02'

//#UPHLICA maxForks 10
//#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'}
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2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -5,7 +5,7 @@ manifest {
name = 'Cecret'
author = 'Erin Young'
homePage = 'https://github.com/UPHL-BioNGS/Cecret'
version = 'v3.13.20240326'
version = 'v3.13.20240402'
defaultBranch = 'master'
recurseSubmodules = false
description = 'Reference-based consensus creation'
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