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jhuapl-bio · Jun 26, 2024 · 4800762 · 4800762
2 parents 6d6b09a + 97362b1
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diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
 
 ## About
 
-TaxTriage a flexible, containerized bioinformatics pipeline for identification of pathogens within short- or long-read metagenomic sequence data, generated from complex samples/specimens (e.g., respiratory swabs, lesion swabs, whole blood). The workflow includes various software packages to perform quality control, classification, read mapping, as well as generation of confidence metrics and a final report listing anticipated pathogens of relevance. 
+TaxTriage a flexible, containerized bioinformatics pipeline for identification of pathogens within short- (Illumina) or long-read (ONT, PacBio) metagenomic sequence data, generated from complex samples/specimens (e.g., respiratory swabs, lesion swabs, whole blood). The workflow includes various software packages to perform quality control, classification, read mapping, as well as generation of confidence metrics and a final report listing anticipated pathogens of relevance. 
 
 ![](assets/taxtriage_schematics.png)
 

diff --git a/conf/modules.config b/conf/modules.config
@@ -88,6 +88,10 @@ process {
         ext.singularity_pull_docker_container = true
         errorStrategy = 'ignore'
     }
+    withName: MAP_TAXID_ASSEMBLY {
+        ext.singularity_pull_docker_container = true
+        errorStrategy = 'ignore'
+    }
     withName: ORGANISM_MERGE_REPORT {
         ext.singularity_pull_docker_container = true
         errorStrategy = 'ignore'

diff --git a/docs/usage.md b/docs/usage.md
@@ -76,7 +76,7 @@ Unless you are using Seqera, most of the temporary directories and final outputs
 | Column               | Description                                                                                                                                                                            |
 | -------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | `sample`             | **MANDATORY** Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). |
-| `platform`           | **MANDATORY** Platform used, [ILLUMINA, OXFORD]. If omitted or left blank, assumes ILLUMINA                                                                                                                                                     |
+| `platform`           | **MANDATORY** Platform used, [ILLUMINA, OXFORD]. If omitted or left blank, assumes ILLUMINA. If using PacBio, specify OXFORD. An additional update in the near future will allow PACBIO as an input but has not yet been integrated.                                                                                                                                                   |
 | `fastq_1`            | **MANDATORY** Full path to FastQ file for Illumina short reads 1 OR OXFORD reads. File MUST be gzipped and have the extension ".fastq.gz" or ".fq.gz".               |
 | `fastq_2`            | OPTIONAL Full path to FastQ file for Illumina short reads 2. File MUST be gzipped and have the extension ".fastq.gz" or ".fq.gz".                                                     |
 | `trim`               | OPTIONAL TRUE/FALSE, do you want to run trimming on the sample?                                                                                                                                 |