bugfix on screen reads

configs/local.config

@@ -11,7 +11,7 @@ process {
     withLabel:  guppy_gpu   { cpus = params.max_cores }
     withLabel:  kraken2     { cpus = params.cores }
     withLabel:  krona       { cpus = 1 }
-    withLabel:  lcs_sc2     { cpus = params.max_cores } //max_cores
+    withLabel:  lcs_sc2     { cpus = params.max_cores; memory = params.memory } //max_cores
     withLabel:  minimap2    { cpus = params.cores }    
     withLabel:  nanoplot    { cpus = params.cores }
     withLabel:  nextclade   { cpus = params.cores }

nextflow.config

@@ -113,7 +113,7 @@ profiles {
             memory = params.memory
         }
 
-        process.errorStrategy = 'ignore'
+        //process.errorStrategy = 'ignore'
     }
 
     slurm {

poreCov.nf

@@ -273,11 +273,11 @@ else { params.pangolindocker = params.defaultpangolin ; params.nextcladedocker =
 if ( params.screen_reads && params.lcs_ucsc_update ){
     if ( internetcheck.toString() == "true" ) { 
         latest_version = 'https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/public-latest.version.txt'.toURL().text.split('\\(')[1].split('\\)')[0]
-        println "\033[0;32mFound latest UCSC version, using: " + latest_version + " \033[0m" 
+        log.info "\033[0;32mFound latest UCSC version, using: " + latest_version + " \033[0m" 
         params.lcs_ucsc = latest_version
     }
     if ( internetcheck.toString() == "false" ) { 
-        println "\033[0;33mCould not find the latest UCSC version, trying: " + params.lcs_ucsc_version + "\033[0m"
+        log.info "\033[0;33mCould not find the latest UCSC version, trying: " + params.lcs_ucsc_version + "\033[0m"
         params.lcs_ucsc = params.lcs_ucsc_version
     }
 } else { params.lcs_ucsc = params.lcs_ucsc_version}

workflows/process/lcs_sc2.nf

@@ -12,7 +12,7 @@ process lcs_ucsc_markers_table {
         """
         git clone https://github.com/rki-mf1/LCS.git --branch 2023.01.30
 
-        if [[ "${variant_group_tsv}" != default ]]; then
+        if [[ "${params.lcs_variant_groups}" != default ]]; then
             rm -rf LCS/data/variant_groups.tsv
             cp ${variant_group_tsv} LCS/data/variant_groups.tsv
         fi
@@ -22,6 +22,7 @@ process lcs_ucsc_markers_table {
         sed -i "s/PB_VERSION=.*/PB_VERSION='${params.lcs_ucsc}'/" rules/config.py
         sed -i "s/NUM_SAMPLE=.*/NUM_SAMPLE=${params.lcs_ucsc_downsampling}/" rules/config.py
         mem=\$(echo ${task.memory} | cut -d' ' -f1)
+        echo \$mem
         ## run pipeline
         snakemake --cores ${task.cpus} --resources mem_gb=\$mem --config dataset=somestring markers=ucsc -- ucsc_gather_tables
         ## output

workflows/read_classification.nf

@@ -8,6 +8,7 @@ workflow read_classification_wf {
         fastq
     main: 
 
+    // Check for human contamination
         // database download
         if (params.krakendb) { kraken_db = file("${params.krakendb}") }
         else  { download_database_kraken2(); kraken_db = download_database_kraken2.out } 
@@ -18,19 +19,17 @@ workflow read_classification_wf {
         // visuals
         krona(kraken2.out)
 
+    // Metagenomic analysis
         // calculate mixed/ pooled samples using LCS, https://github.com/rvalieris/LCS
         if (params.screen_reads) {
-            if (params.lcs_variant_groups == 'default'){
-                lcs_variant_groups_ch = Channel.empty()
-            } else {
-                lcs_variant_groups_ch = Channel.fromPath("${params.lcs_variant_groups}", checkIfExists: true) 
-            }
+            if (params.lcs_variant_groups == 'default')     { lcs_variant_groups_ch = Channel.empty() } 
+            else                                            { lcs_variant_groups_ch = Channel.fromPath("${params.lcs_variant_groups}", checkIfExists: true)}
+
             lcs_ucsc_markers_table(lcs_variant_groups_ch.ifEmpty([]))
             lcs_sc2(fastq.combine(lcs_ucsc_markers_table.out))
             lcs_output = lcs_sc2.out
-        } else {
-            lcs_output = Channel.empty()
-        }
+        } 
+        else { lcs_output = Channel.empty()}
 
     emit:   
         kraken = kraken2.out