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Merged
kathrynmurie merged 3 commits into from
Feb 18, 2026
Merged

Develop #67

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2d34d20
update docker image reference
kathrynmurie Feb 17, 2026
916735b
remove TODO comments
kathrynmurie Feb 17, 2026
fb03a78
update logo in readme
kathrynmurie Feb 17, 2026
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3 changes: 1 addition & 2 deletions Mad4Hatter.wdl
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Expand Up @@ -46,8 +46,7 @@ workflow MAD4HatTeR {
String output_directory
Int dada2_additional_memory = 0
String? dada2_runtime_size
# TODO: Pin the specific docker image version here when first release is ready
String docker_image = "eppicenter/mad4hatter:develop"
String docker_image = "eppicenter/mad4hatter:v1.0.0"
}

# Use sub() with a regular expression to check for valid characters in output_directory
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3 changes: 1 addition & 2 deletions Mad4HatterPostProcessing.wdl
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Expand Up @@ -18,8 +18,7 @@ workflow Mad4HatterPostProcessing {
Boolean mask_homopolymers = true
File? masked_fasta
File pool_options_json = "/opt/mad4hatter/conf/terra_panel.json" # Optional custom pool options JSON file. Needs to be on docker image.
# TODO: Pin the specific docker image version here when first release is ready
String docker_image = "eppicenter/mad4hatter:develop"
String docker_image = "eppicenter/mad4hatter:v1.0.0"
}

# Check that either one of genome or refseq_fasta is provided or nothing is provided (then refseq_fasta is auto-generated)
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3 changes: 1 addition & 2 deletions Mad4HatterQcOnly.wdl
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Expand Up @@ -14,8 +14,7 @@ workflow Mad4HatterQcOnly {
Boolean gtrim = false
Int quality_score = 20
Int allowed_errors = 0
# TODO: Pin the specific docker image version here when first release is ready
String docker_image = "eppicenter/mad4hatter:develop"
String docker_image = "eppicenter/mad4hatter:v1.0.0"
}

File pool_options_json = "/opt/mad4hatter/conf/terra_panel.json" # Optional custom pool options JSON file. Needs to be on docker image.
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2 changes: 1 addition & 1 deletion README.md
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@@ -1,4 +1,4 @@
# MAD4HATTER <img src="https://github.com/EPPIcenter/mad4hatter/blob/gh-pages/logo.svg" alt="Mad4hatter logo" height="80">
# MAD4HATTER <img src="https://github.com/EPPIcenter/wonderland-docs/blob/main/docs/assets/logo.svg" alt="Mad4hatter logo" height="80">

**Mad4hatter** is a bioinformatics pipeline designed to analyse *Plasmodium* Illumina amplicon sequencing data. It processes raw FASTQ files and produces an allele table, core QC metrics, and drug-resistance information. It was originally developed for the [MAD4HatTeR panel](https://doi.org/10.1038/s41598-025-94716-5) but has since been adapted to support additional panels. While the pipeline can be run on any panel, it was optimised using MAD4HatTeR data; panels with substantially different properties, such as very short amplicon targets, may require additional tuning to achieve optimal performance. Several commonly used panels are preconfigured for convenience, and new panels can be easily added through simple configuration (see below). If you are using a pre-configured panel, simply provide your FASTQ files and the panel name, and you’re ready to run!

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