Strict syntax

conf/base.config

@@ -86,10 +86,6 @@ process {
         time   = { 4.h  * task.attempt }
     }
 
-    withName:CUSTOM_DUMPSOFTWAREVERSIONS {
-        cache = false
-    }
-
     // IN CASES WHERE THERE IS ONE HIC FILE THIS WILL NEED ALMOST NOTHING
     withName:SAMTOOLS_MERGE {
         cpus    = { 16    * 1 }
@@ -226,7 +222,7 @@ process {
         memory  = { 128.MB * Math.ceil( task.attempt * 1.5 ) }
     }
 
-    withName: JUICER_TOOLS_PRE {
+    withName: JUICERTOOLS_PRE {
         cpus    = { 20     * task.attempt }
         memory  = { 100.GB * task.attempt }
     }

conf/modules.config

@@ -11,17 +11,10 @@
 */
 
 process {
-    withName: CUSTOM_DUMPSOFTWAREVERSIONS {
-        publishDir = [
-            path: { "${params.outdir}/${task.process.tokenize(":")[-1].tokenize("_")[0].toLowerCase()}" },
-            mode: params.publish_dir_mode,
-            pattern: "*_versions.yml"
-        ]
-    }
 
     // Files to be uploaded to the TreeVal JBrowse2 instance
     // .genome, .gz.{tbi|csi}, .bigBed, .bigWig, .paf
-    withName: "GENERATE_GENOME|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED|UCSC_BEDGRAPHTOBIGWIG|BED2BW_NORMAL|.*:SYNTENY:MINIMAP2_ALIGN|.*:.*:GENERATE_SORTED_GENOME:GNU_SORT|CUSTOM_GETCHROMSIZES" {
+    withName: "GENERATE_GENOME|TABIX_BGZIPTABIX|UCSC_BEDTOBIGBED|UCSC_BEDGRAPHTOBIGWIG|BED2BW_NORMAL|.*:SYNTENY:MINIMAP2_ALIGN" {
         publishDir = [
             path: { "${params.outdir}/treeval_upload" },
             mode: params.publish_dir_mode,
@@ -94,12 +87,6 @@ process {
         ext.suffix = 'fasta'
     }
 
-    withName: 'GAWK_CLEAN_TELOMERE' {
-        ext.args2  = { "'/^>/'" }        // Keep lines starting with '>'
-        ext.prefix = { "${meta.id}_CLEANED" }
-        ext.suffix = 'telomere'          // Must end with telomere otherwise FIND_TELOMERE_WINDOWS will crash
-    }
-
     withName: 'GAWK_MAP_TELO' {
         ext.args2 = { "-v OFS=\"\t\" 'BEGIN { sub(/^>/, \"\"); print \$1, \$4, \$5, \$6 }'" }
         ext.prefix   = { "${meta.id}_map_telo" }
@@ -201,7 +188,7 @@ process {
 
     withName: GNU_SORT_B {
         ext.args        = { "-k1,1 -k2,2n -S${task.memory.mega - 100}M -T ." }
-        ext.suffix      = { "sorted.genome" }
+        ext.suffix      = { "sorted" }
     }
 
     withName: GNU_SORT_C {
@@ -257,7 +244,7 @@ process {
 
     withName: ".*:.*:(GEN_ALIGNMENTS|RNA_ALIGNMENTS|CDS_ALIGNMENTS):MINIMAP2_ALIGN" {
         ext.args        = {"-x splice ${meta.intron_size ? "-G ${meta.intron_size}" : "" } ${reference.size() > 2.5e9 ? (" -I " + Math.ceil(reference.size()/1e9)+"G") : ""} "}
-        ext.args2       = { "-T ${meta.id}_tmp" }
+        // ext.args2       = { "-T ${meta.id}_tmp" }
         ext.prefix      = { "${meta.id}_alignment_${reference.getName().tokenize(".")[0]}" }
     }
 
@@ -309,7 +296,7 @@ process {
     //
     withName: ".*:SYNTENY:MINIMAP2_ALIGN" {
         ext.args        = "-t 8 -x asm10"
-        ext.args2       = { "-T ${meta.id}_tmp" }
+        // ext.args2       = { "-T ${meta.id}_tmp" }
         ext.prefix      = { "${meta.id}_synteny_${reference.getName().tokenize(".")[0]}" }
     }
 
@@ -416,7 +403,7 @@ process {
     // normal = standard run, pi = "pre-ingestion", hr = High res
     //
     withName: PRETEXTMAP_STANDRD {
-        ext.args        = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0 --memory ${task.memory.giga}" }
+        ext.args        = { "${meta.map_order.equals("length") ? "--sortby length": "--sortby nosort" } --mapq 0" }
         ext.prefix      = { "${meta.id}_normal_pi" }
     }
 
@@ -449,38 +436,29 @@ process {
         ext.prefix      = { "${meta.id}_normal" }
     }
 
-
-    withName: JUICER_TOOLS_PRE {
-        ext.juicer_tools_jar    = "juicer_tools.1.8.9_jcuda.0.8.jar"
-        ext.juicer_jvm_params   = "-Xms1g -Xmx36g"
-    }
-
     withName: COOLER_CLOAD {
-        ext.args        = "pairs -0 -c1 3 -p1 4 -c2 7 -p2 8"
+        ext.args        = "-0 -c1 3 -p1 4 -c2 7 -p2 8"
     }
 
     withName: ".*:.*:(HIC_BAMTOBED_COOLER|HIC_BAMTOBED_JUICER):SAMTOOLS_MARKDUP" {
         ext.prefix      = { "${meta.id}_mkdup" }
     }
 
     withName: ".*:.*:HIC_BWAMEM2:CRAM_FILTER_ALIGN_BWAMEM2_FIXMATE_SORT" {
-        ext.args        = ""
-        ext.args1       = "-F0xB00 -nt"
-        ext.args2       = { "-5SPCp -H'${rglines}'" }
-        ext.args3       = "-mpu"
-        ext.args4       = { "--write-index -l1" }
+        ext.args       = "-F0xB00 -nt"
+        ext.args1       = "-mpu"
+        ext.args2       = { "--write-index -l1" }
     }
 
     withName: ".*:.*:HIC_BWAMEM2:SAMTOOLS_MERGE" {
         ext.prefix      = { "${meta.id}_hic_bwamem2_merge" }
     }
 
     withName: ".*:.*:HIC_MINIMAP2:CRAM_FILTER_MINIMAP2_FILTER5END_FIXMATE_SORT" {
-        ext.args        = ""
-        ext.args1       = ""
-        ext.args2       = { "-ax sr" }
-        ext.args3       = "-mpu"
-        ext.args4       = { "--write-index -l1" }
+        ext.args       = ""
+        ext.args1       = { "-ax sr" }
+        ext.args2       = "-mpu"
+        ext.args3       = { "--write-index -l1" }
     }
 
     withName: ".*:.*:HIC_MINIMAP2:SAMTOOLS_MERGE" {

main.nf

@@ -26,11 +26,6 @@ workflow {
 
     main:
 
-    params.mode      = params.mode ?: "FULL"
-    params.binfile   = params.binfile ?: false
-    params.juicer    = params.juicer ?: false
-    params.run_hires = params.run_hires ?: true
-
     //
     // SUBWORKFLOW: Run initialisation tasks
     //
@@ -54,7 +49,6 @@ workflow {
     // WORKFLOW: Run main workflow
     //
     SANGERTOL_TREEVAL (
-        PIPELINE_INITIALISATION.out.assembly_id,
         PIPELINE_INITIALISATION.out.reference,
         PIPELINE_INITIALISATION.out.map_order,
         PIPELINE_INITIALISATION.out.assem_reads,