Allow optional output from ampli_clean

main.nf

@@ -1,5 +1,5 @@
 process ampliClean {
-  container "${params.wf.container}@${params.wf.container_sha}"
+  container "${params.wf.container}"
 
   publishDir path: "${params.out_dir}/${barcode}/ampli_clean", mode: 'copy'
 
@@ -12,16 +12,18 @@ process ampliClean {
 
 
   output:
-    tuple val("${barcode}"), path("${barcode}.*.fastq.gz")
+    tuple val("${barcode}"), path("${barcode}.*.fastq.gz"), emit: reads, optional: true
+    path "log.txt"
 
   script:
     """
-    ampli_clean -f ${binned_reads} -r ${refs} -o ${barcode} -b ${bed} --min ${min} --max ${max} -s --fastq
+    ampli_clean -f ${binned_reads} -r ${refs} -o ${barcode} -b ${bed} --min ${min} --max ${max} -s --fastq --log
     """
 }
 
 process articMinion {
-  container "${params.wf.container}@${params.wf.container_sha}"
+  container "${params.wf.container}"
+  //container "${params.wf.container}@${params.wf.container_sha}"
 
   publishDir path: "${params.out_dir}/${barcode}/artic", mode: 'copy'
 
@@ -60,5 +62,5 @@ workflow {
 
 //Run the processes
   ampliClean(barcode_input, ref_ch, bed_ch, min_ch, max_ch)
-  articMinion(ampliClean.out, schemes_dir_ch, med_mod_ch)
+  articMinion(ampliClean.out.reads, schemes_dir_ch, med_mod_ch)
 }

nextflow.config

@@ -40,8 +40,8 @@ params {
               "--fastq test_data/barcode01/reads.fastq.gz",
           ]
           agent = null
-          container = "rmcolq/artic_rsv"
-          container_sha = "sha256:ce049e449ed09e8538d246fb2e7a8fb3a58d883092293c7f689ab445e5596cb2"
+          container = "dmmalone/artic_rsv:0.0.1"
+          //container_sha = "sha256:c8a132a673710adef24fdeae9d0cd6e28c92c5b4ed3933b2f61a67f0826b4968"
         }
 }
 
@@ -173,18 +173,22 @@ process.shell = ['/bin/bash', '-euo', 'pipefail']
 
 timeline {
     enabled = true
+    overwrite = true
     file    = "${params.out_dir}/execution/timeline.html"
 }
 report {
     enabled = true
+    overwrite = true
     file    = "${params.out_dir}/execution/report.html"
 }
 trace {
     enabled = true
+    overwrite = true
     file    = "${params.out_dir}/execution/trace.txt"
 }
 dag {
     enabled = true
+    overwrite = true
     file    = "${params.out_dir}/execution/pipeline_dag.html"
 }