Mercurial > repos > kkonganti > cfsan_centriflaken

changeset 93:3f367a0de778

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:14:15 -0400
parents 295c2597a475
children ca861be31596
files 0.3.0/conf/modules.config 0.3.0/nextflow.config 0.3.0/workflows/conf/centriflaken.config 0.3.0/workflows/conf/centriflaken_hy.config
diffstat 4 files changed, 25 insertions(+), 49 deletions(-) [+]
line wrap: on
line diff
--- a/0.3.0/conf/modules.config	Tue Jul 19 10:07:24 2022 -0400
+++ b/0.3.0/conf/modules.config	Tue Jul 19 10:14:15 2022 -0400
@@ -14,78 +14,54 @@
         ![0].contains(task.exitStatus) ? dynamic_retry(task.attempt, 10) : 'finish'
     }
 
-    maxRetries = 1
+    maxRetries = 80
 
     withLabel: 'process_femto' {
-        cpus = { 1 * task.attempt }
-        memory = { 1.GB * task.attempt }
-        time = { 1.h * task.attempt }
+        cpus = 2
     }
 
     withLabel: 'process_pico' {
-        cpus = { 2 * task.attempt }
-        memory = { 4.GB * task.attempt }
-        time = { 2.h * task.attempt }
+        cpus = 2
     }
 
     withLabel: 'process_nano' {
-        cpus = { 4 * task.attempt }
-        memory = { 8.GB * task.attempt }
-        time = { 4.h * task.attempt }
+        cpus = 4
     }
 
     withLabel: 'process_micro' {
-        cpus = { 8 * task.attempt }
-        memory = { 16.GB * task.attempt }
-        time = { 8.h * task.attempt }
+        cpus = 8
     }
 
     withLabel: 'process_only_mem_low' {
-        cpus = { 1 * task.attempt }
-        memory = { 60.GB * task.attempt }
-        time = { 20.h * task.attempt }
+        cpus = 2
     }
 
     withLabel: 'process_only_mem_medium' {
-        cpus = { 1 * task.attempt }
-        memory = { 100.GB * task.attempt }
-        time = { 30.h * task.attempt }
+        cpus = 2
     }
 
     withLabel: 'process_only_mem_high' {
-        cpus = { 1 * task.attempt }
-        memory = { 128.GB * task.attempt }
-        time = { 60.h * task.attempt }
+        cpus = 2
     }
 
     withLabel: 'process_low' {
-        cpus = { 10 * task.attempt }
-        memory = { 60.GB * task.attempt }
-        time = { 20.h * task.attempt }
+        cpus = 8
     }
 
     withLabel: 'process_medium' {
-        cpus = { 10 * task.attempt }
-        memory = { 100.GB * task.attempt }
-        time = { 30.h * task.attempt }
+        cpus = 8
     }
 
     withLabel: 'process_high' {
-        cpus = { 10 * task.attempt }
-        memory = { 128.GB * task.attempt }
-        time = { 60.h * task.attempt }
+        cpus = 8
     }
 
     withLabel: 'process_higher' {
-        cpus = { 10 * task.attempt }
-        memory = { 256.GB * task.attempt }
-        time = { 60.h * task.attempt }
+        cpus = 8
     }
 
     withLabel: 'process_gigantic' {
-        cpus = { 10 * task.attempt }
-        memory = { 512.GB * task.attempt }
-        time = { 60.h * task.attempt }
+        cpus = 8
     }
 }
 
--- a/0.3.0/nextflow.config	Tue Jul 19 10:07:24 2022 -0400
+++ b/0.3.0/nextflow.config	Tue Jul 19 10:14:15 2022 -0400
@@ -27,8 +27,8 @@
 includeConfig "${pd}${fs}conf${fs}modules.config"
 
 // Nextflow runtime profiles
-conda.cacheDir = '/tmp'
-singularity.cacheDir = '/tmp'
+conda.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/kondagac_cache'
+singularity.cacheDir = '/tool/tool-data/cfsan-centriflaken-db/0/cingularitygac_cache'
 
 profiles {
     standard {
--- a/0.3.0/workflows/conf/centriflaken.config	Tue Jul 19 10:07:24 2022 -0400
+++ b/0.3.0/workflows/conf/centriflaken.config	Tue Jul 19 10:14:15 2022 -0400
@@ -2,13 +2,13 @@
     workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
     workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
     workflow_version = '0.2.0'
-    centrifuge_x = '/hpc/db/centrifuge/2022-04-12/ab'
+    centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
     centrifuge_extract_bug = 'Escherichia coli'
     centrifuge_save_aligned = false
     centrifuge_save_unaligned = false
     centrifuge_out_fmt_sam = false
     centrifuge_ignore_quals = false
-    kraken2_db = '/hpc/db/kraken2/standard-210914'
+    kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
     kraken2_confidence = '0.0'
     kraken2_quick = false
     kraken2_use_mpa_style = false
@@ -34,7 +34,7 @@
     ectyper_perc_opcov = 95
     ectyper_perc_hpcov = 50
     serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
-    serotypefinder_db = '/hpc/db/serotypefinder/2.0.2'
+    serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
     serotypefinder_min_cov = 0.80
     serotypefinder_min_threshold = 0.85
     serotypefinder_x = true
@@ -48,10 +48,10 @@
     mlst_mincov = 10
     mlst_minscore = 50
     amrfinderplus_run = false
-    amrfinderplus_db = '/hpc/db/amrfinderplus/3.10.24/latest'
+    amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
     amrfinderplus_genes = true
     abricate_run = true
-    abricate_datadir = '/hpc/db/abricate/1.0.1/db'
+    abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
     abricate_minid = 90
     abricate_mincov = 80
     abricate_summary_run = true
--- a/0.3.0/workflows/conf/centriflaken_hy.config	Tue Jul 19 10:07:24 2022 -0400
+++ b/0.3.0/workflows/conf/centriflaken_hy.config	Tue Jul 19 10:14:15 2022 -0400
@@ -2,13 +2,13 @@
     workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
     workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
     workflow_version = '0.3.0'
-    centrifuge_x = '/hpc/db/centrifuge/2022-04-12/ab'
+    centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
     centrifuge_extract_bug = 'Escherichia coli'
     centrifuge_save_aligned = false
     centrifuge_save_unaligned = false
     centrifuge_out_fmt_sam = false
     centrifuge_ignore_quals = false
-    kraken2_db = '/hpc/db/kraken2/standard-210914'
+    kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
     kraken2_confidence = '0.0'
     kraken2_quick = false
     kraken2_use_mpa_style = false
@@ -55,7 +55,7 @@
     ectyper_perc_opcov = 95
     ectyper_perc_hpcov = 50
     serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
-    serotypefinder_db = '/hpc/db/serotypefinder/2.0.2'
+    serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
     serotypefinder_min_cov = 0.80
     serotypefinder_min_threshold = 0.85
     serotypefinder_x = true
@@ -69,10 +69,10 @@
     mlst_mincov = 10
     mlst_minscore = 50
     amrfinderplus_run = false
-    amrfinderplus_db = '/hpc/db/amrfinderplus/3.10.24/latest'
+    amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
     amrfinderplus_genes = true
     abricate_run = true
-    abricate_datadir = '/hpc/db/abricate/1.0.1/db'
+    abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
     abricate_minid = 90
     abricate_mincov = 80
     abricate_summary_run = true