Increased internet download timeout

Author: olabiyi

Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/workflow_code/bin/Illumina-PE-R-processing.R

@@ -60,6 +60,9 @@ library(dada2); packageVersion("dada2")
 library(DECIPHER); packageVersion("DECIPHER")
 library(biomformat); packageVersion("biomformat")
 
+# Set default internet timeout to 1 hour
+options(timeout=3600)
+
     ### general processing ###
     # reading in unique sample names into variable
 sample.names <- scan(sample_IDs_file, what="character")

Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/workflow_code/bin/Illumina-SE-R-processing.R

@@ -50,6 +50,9 @@ library(dada2); packageVersion("dada2")
 library(DECIPHER); packageVersion("DECIPHER")
 library(biomformat); packageVersion("biomformat")
 
+# Set default internet timeout to 1 hour
+options(timeout=3600)
+
     ### general processing ###
     # reading in unique sample names into variable
 sample.names <- scan(sample_IDs_file, what="character")

Amplicon/Illumina/Workflow_Documentation/SW_AmpIllumina-B/workflow_code/modules/zip_biom.nf

@@ -13,11 +13,11 @@ process ZIP_BIOM {
     input:
        path(taxonomy_and_counts_biom)
     output:
-        path("taxonomy-and-counts_${params.assay_suffix}.biom.zip"), emit: biom
+        path("taxonomy-and-counts${params.assay_suffix}.biom.zip"), emit: biom
         path("versions.txt"), emit: version
     script:
         """
-        zip -j -q taxonomy-and-counts_${params.assay_suffix}.biom.zip \\
+        zip -j -q taxonomy-and-counts${params.assay_suffix}.biom.zip \\
                 ${taxonomy_and_counts_biom}
 
         zip -h | grep "Zip" | sed -E 's/(Zip.+\\)).+/\\1/' > versions.txt