Merge branch 'CW-2117-process-all-samples' into 'dev'

CW-2117 Process all samples

Closes CW-2117

See merge request epi2melabs/workflows/wf-artic!137

CHANGELOG.md

@@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.3.28]
+### Fixed
+- Fixed an error which was causing only a single sample to be processed, instead of all samples in the input FASTQ directory
+
 ## [v0.3.27]
 ### Added
 - Configuration for running demo data in AWS

main.nf

@@ -37,9 +37,8 @@ process runArtic {
     label "artic"
     cpus params.artic_threads
     input:
-        tuple val(meta), path(fastq_file), path(fastq_stats)
+        tuple val(meta), path(fastq_file), path(fastq_stats), val(medaka_model)
         path scheme_dir
-        val(medaka_model)
     output:
         path "${meta.alias}.consensus.fasta", emit: consensus
         path "${meta.alias}.depth.txt", emit: depth_stats
@@ -415,7 +414,8 @@ workflow pipeline {
                 workflow_params)
             results = html_doc[0].concat(html_doc[1])
         } else {
-            artic = runArtic(samples, scheme_dir, medaka_variant_model)
+            samples_for_artic = samples.combine(medaka_variant_model)
+            artic = runArtic(samples_for_artic, scheme_dir)
             all_depth = combineDepth(artic.depth_stats.collect())
             // collate consensus and variants
             all_consensus = allConsensus(artic.consensus.collect())

nextflow.config

@@ -71,7 +71,7 @@ manifest {
     description     = 'Run the ARTIC SARS-CoV-2 methodology on multiplexed MinION, GridION, and PromethION data.'
     mainScript      = 'main.nf'
     nextflowVersion = '>=20.10.0'
-    version         = 'v0.3.27'
+    version         = 'v0.3.28'
 }
 
 epi2melabs {