# HG changeset patch
# User rliterman
# Date 1733338093 18000
# Node ID 893a6993efe34a464d71d8ad8f62f64678af9477
# Parent  792274118b2ed28655a6c0f900fb774153aaceab
"planemo upload"

diff -r 792274118b2e -r 893a6993efe3 CSP2/bin/chooseRefs.py
--- a/CSP2/bin/chooseRefs.py	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/bin/chooseRefs.py	Wed Dec 04 13:48:13 2024 -0500
@@ -85,7 +85,7 @@
 parser = argparse.ArgumentParser(description='Choose reference isolates based on FASTA metrics and mean distances.')
 parser.add_argument('--ref_count', type=int, default=1, help='Number of reference isolates to select')
 parser.add_argument('--mash_triangle_file', type=str, help='Path to the mash triangle file')
-parser.add_argument('--trim_name', type=str, default="", help='trim name')
+parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
 args = parser.parse_args()
 
 ref_count = args.ref_count
diff -r 792274118b2e -r 893a6993efe3 CSP2/bin/fetchReads.py
--- a/CSP2/bin/fetchReads.py	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/bin/fetchReads.py	Wed Dec 04 13:48:13 2024 -0500
@@ -11,7 +11,7 @@
 parser.add_argument('--read_filetype',default='fastq.gz', type=str, help='read filetype information')
 parser.add_argument('--forward_suffix',default='_1.fastq.gz', type=str, help='forward suffix')
 parser.add_argument('--reverse_suffix',default = '_2.fastq.gz', type=str, help='reverse suffix')
-parser.add_argument('--trim_name', type=str, default="", help='trim name')
+parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
 args = parser.parse_args()
 
 # Get path to directory containing read files
diff -r 792274118b2e -r 893a6993efe3 CSP2/bin/runSNPPipeline.py
--- a/CSP2/bin/runSNPPipeline.py	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/bin/runSNPPipeline.py	Wed Dec 04 13:48:13 2024 -0500
@@ -643,7 +643,7 @@
 parser.add_argument('--query_edge', default=150,type=int, help='Query edge')
 parser.add_argument('--density_windows', default="1000,125,15",type=str, help='Density windows')
 parser.add_argument('--max_snps', default="3,2,1", type=str, help='Maximum SNPs')
-parser.add_argument('--trim_name', type=str, default="", help='trim name')
+parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
 parser.add_argument('--max_missing',default=50, type=float, help='Maximum missing')
 parser.add_argument('--tmp_dir',default="", type=str, help='Temporary directory')
 parser.add_argument('--rescue', default="norescue",type=str, help='Rescue edge SNPs (rescue/norescue)')
diff -r 792274118b2e -r 893a6993efe3 CSP2/bin/saveSNPDiffs.py
--- a/CSP2/bin/saveSNPDiffs.py	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/bin/saveSNPDiffs.py	Wed Dec 04 13:48:13 2024 -0500
@@ -30,7 +30,7 @@
 parser.add_argument("--snpdiffs_file", help="Path to the SNP diffs list file")
 parser.add_argument("--summary_file", help="Path to the summary file")
 parser.add_argument("--isolate_file", help="Path to the isolate data file")
-parser.add_argument('--trim_name', type=str, default="", help='trim name')
+parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
 parser.add_argument("--ref_id_file", help="Path to the reference IDs file")
 args = parser.parse_args()
 
diff -r 792274118b2e -r 893a6993efe3 CSP2/bin/screenSNPDiffs.py
--- a/CSP2/bin/screenSNPDiffs.py	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/bin/screenSNPDiffs.py	Wed Dec 04 13:48:13 2024 -0500
@@ -555,7 +555,7 @@
 parser.add_argument("--query_edge", default=150,type=int, help="Query edge")
 parser.add_argument("--density_windows",default="1000,125,15", help="Density windows (comma-separated)")
 parser.add_argument("--max_snps", default="3,2,1",help="Maximum SNPs (comma-separated)")
-parser.add_argument('--trim_name', type=str, default="", help='trim name')
+parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
 parser.add_argument("--output_file", help="Output file")
 parser.add_argument("--ref_id", help="Reference IDs file")
 parser.add_argument("--tmp_dir",default="", help="TMP dir")
diff -r 792274118b2e -r 893a6993efe3 CSP2/bin/userSNPDiffs.py
--- a/CSP2/bin/userSNPDiffs.py	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/bin/userSNPDiffs.py	Wed Dec 04 13:48:13 2024 -0500
@@ -31,7 +31,7 @@
 
 parser = argparse.ArgumentParser()
 parser.add_argument("--snpdiffs_file", help="Path to the SNP diffs list file")
-parser.add_argument('--trim_name', type=str, default="", help='trim name')
+parser.add_argument('--trim_name', nargs='?', const="", default="", type=str, help='Trim name')
 args = parser.parse_args()
 
 snpdiffs_list_file = args.snpdiffs_file
diff -r 792274118b2e -r 893a6993efe3 CSP2/conf/profiles.config
--- a/CSP2/conf/profiles.config	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/conf/profiles.config	Wed Dec 04 13:48:13 2024 -0500
@@ -90,7 +90,7 @@
         executor.$slurm.exitReadTimeout = 120000
 
         process.executor = 'slurm'
-        params.cores = 8
+        params.cores = 1
         params.python_module = ""
         params.mummer_module = ""
         params.skesa_module = ""
diff -r 792274118b2e -r 893a6993efe3 CSP2/nextflow.config
--- a/CSP2/nextflow.config	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/nextflow.config	Wed Dec 04 13:48:13 2024 -0500
@@ -15,12 +15,14 @@
 // CPU/memory settings
 process {
     withLabel: 'mummerMem' {
+        task_name = 'CSP2-MUMmer'
         cpus = 1
-       // memory = '4 GB'
+        //memory = '4 GB'
     }
-    //withLabel: 'skesaMem' {
-    //    memory = '12 GB'
-    //}
+    withLabel: 'skesaMem' {
+        task_name = 'CSP2-SKESA'
+        //memory = '12 GB'
+    }
 }
 
 // Global default params
diff -r 792274118b2e -r 893a6993efe3 CSP2/subworkflows/fetchData/main.nf
--- a/CSP2/subworkflows/fetchData/main.nf	Wed Dec 04 12:50:59 2024 -0500
+++ b/CSP2/subworkflows/fetchData/main.nf	Wed Dec 04 13:48:13 2024 -0500
@@ -20,7 +20,8 @@
 userSNPDiffs = file("${projectDir}/bin/userSNPDiffs.py")
 
 // Set SKESA cores to 4 or fewer
-skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer
+//skesa_cpus = (params.cores as Integer) >= 4 ? 4 : params.cores as Integer
+skesa_cpus = 1
 
 workflow {
     main:
@@ -499,8 +500,10 @@
     assembled_data = assembly_output.map{it->tuple(it[0],it[3])}
 }
 process skesaAssemble{
-    //label 'skesaMem'
-  
+    label 'skesaMem'
+
+    cpus = skesa_cpus
+    
     input:
     tuple val(sample_name),val(read_type),val(read_location)