Merge pull request #49 from hoelzer/revision-2024

Revision 2024
hoelzer · Feb 16, 2024 · 0af68da · 0af68da
2 parents 350c386 + 18208aa
commit 0af68da
Show file tree

Hide file tree

Showing 29 changed files with 450 additions and 622 deletions.
diff --git a/configs/conda.config b/configs/conda.config
@@ -1,9 +1,9 @@
 process {
     withLabel: basics {     conda = "$baseDir/envs/basics.yaml" } 
     withLabel: bbmap {      conda = "$baseDir/envs/bbmap.yaml" } 
-    withLabel: bwa {        conda = "$baseDir/envs/bwa.yaml" } 
     withLabel: diamond {    conda = "$baseDir/envs/diamond.yaml" } 
     withLabel: prodigal {   conda = "$baseDir/envs/prodigal.yaml" } 
+    withLabel: ubuntu {     conda = "$baseDir/envs/basics.yaml" } 
     withLabel: fastp {      conda = "$baseDir/envs/fastp.yaml" } 
     withLabel: nanoplot {   conda = "$baseDir/envs/nanoplot.yaml" } 
     withLabel: spades {     conda = "$baseDir/envs/spades.yaml" } 
@@ -12,8 +12,6 @@ process {
     withLabel: racon {      conda = "$baseDir/envs/racon.yaml" } 
     withLabel: medaka {     conda = "$baseDir/envs/medaka.yaml" } 
     withLabel: pilon {      conda = "$baseDir/envs/pilon.yaml" } 
-    withLabel: samtools {   conda = "$baseDir/envs/samtools.yaml" } 
-    withLabel: ubuntu {     conda = "$baseDir/envs/basics.yaml" } 
     withLabel: kmc {        conda = "$baseDir/envs/kmc.yaml" } 
     withLabel: ggplot2 {    conda = "$baseDir/envs/ggplot2.yaml" } 
 }
diff --git a/configs/container.config b/configs/container.config
@@ -1,20 +1,19 @@
 process {
     withLabel: basics {     container = 'nanozoo/basics:1.0--da8477a' } 
-    withLabel: bbmap {      container = 'nanozoo/bbmap:38.79--8e915d7' } 
-    withLabel: bwa {        container = 'nanozoo/bwa:0.7.17--d11c0a4' }
+    withLabel: bbmap {      container = 'nanozoo/bbmap:38.79--07fb785' } 
     withLabel: diamond {    container = 'nanozoo/diamond:0.9.14--dc7daf8' }
     withLabel: prodigal {   container = 'nanozoo/prodigal:2.6.3--2769024' }
-    withLabel: fastp {      container = 'nanozoo/fastp:0.20.1--4bf9624' }
-    withLabel: nanoplot {   container = 'nanozoo/nanoplot:1.32.0--1ae6f5d' }
-    withLabel: spades {     container = 'nanozoo/spades:3.14.1--794e6a2'  }
-    withLabel: flye {       container = 'nanozoo/flye:2.8--95b6dca' } 
-    withLabel: minimap2 {   container = 'nanozoo/minimap2:2.17--7066fef' }
-    withLabel: racon {      container = 'nanozoo/racon:1.4.13--bb8a908' } 
-    withLabel: medaka {     container = 'nanozoo/medaka:1.0.3--7c62d67' }
-    withLabel: pilon {      container = 'nanozoo/pilon:1.23--f1b7155' }
-    withLabel: samtools {   container = 'nanozoo/samtools:1.10--9ffc8c9' }
+    withLabel: fastp {      container = 'nanozoo/fastp:0.20.0--78a7c63' }
+    withLabel: nanoplot {   container = 'nanozoo/nanoplot:1.25.0--4e2882f' }
+    withLabel: sourmash {   container = 'nanozoo/sourmash:2.3.0--4257650' }
+    withLabel: spades {     container = 'nanozoo/spades:3.14--c3546a9'  }
+    withLabel: flye {       container = 'nanozoo/flye:2.9.3--973d045' } 
+    withLabel: minimap2 {   container = 'nanozoo/minimap2:2.26--d9ef6b6' }
+    withLabel: racon {      container = 'nanozoo/racon:1.5.0--c32e531' } 
+    withLabel: medaka {     container = 'nanozoo/medaka:1.11.3--5764f18' }
+    withLabel: pilon {      container = 'nanozoo/pilon:1.23--b21026d' }
     withLabel: ubuntu {     container = 'ubuntu:xenial' } 
     withLabel: kmc {        container = 'nanozoo/kmc:3.1.2--fa852dd' } 
-    //withLabel: khmer {    container = 'nanozoo/khmer:3.0.0--4650bf7' }     
+    withLabel: khmer {      container = 'nanozoo/khmer:3.0.0--4650bf7' }     
     withLabel: ggplot2 {    container = 'nanozoo/r_ggplot2:0.1--6405f6d' }
 }
diff --git a/configs/googlegenomics.config b/configs/googlegenomics.config
@@ -0,0 +1,15 @@
+// cloud { preemptible = true }
+    process {   
+        executor = 'google-pipelines'
+        withLabel: basics { cpus = 2 ; memory = '16 GB' }
+        withLabel: fastp { cpus = 12 ; memory = '16 GB' }
+        withLabel: nanoplot { cpus = 8 ; memory = '14 GB' }
+        withLabel: spades { cpus = 32 ; memory = '200 GB' }
+        withLabel: sourmash { cpus = 8 ; memory = '24 GB' }
+        withLabel: flye { cpus = 32 ; memory = '120 GB' } 
+        withLabel: minimap2 { cpus = 8 ; memory = '24 GB' }
+        withLabel: racon { cpus = 20 ; memory = '60 GB' } 
+        withLabel: medaka { cpus = 20 ; memory = '40 GB' } 
+        withLabel: ubuntu { cpus = 4 ; memory = '8 GB' } 
+        withLabel: kmc { cpus = 8 ; memory = '16 GB' } 
+    }
diff --git a/configs/local.config b/configs/local.config
@@ -1,7 +1,6 @@
 process {
     withLabel: basics {     cpus = 1 } 
     withLabel: bbmap {      cpus = params.cores; memory = params.memory } 
-    withLabel: bwa {        cpus = params.cores; memory = params.memory } 
     withLabel: fastp {      cpus = params.cores }
     withLabel: prodigal {   cpus = params.cores }
     withLabel: diamond {    cpus = params.cores }
@@ -11,10 +10,10 @@ process {
     withLabel: spades {     cpus = params.cores; memory = params.memory }
     withLabel: flye {       cpus = params.cores; memory = params.memory } 
     withLabel: minimap2 {   cpus = params.cores }
-    withLabel: racon {      cpus = params.cores; memory = params.memory } 
-    withLabel: samtools {   cpus = params.cores; memory = params.memory } 
-    withLabel: medaka {     cpus = params.cores; memory = params.memory }
+    withLabel: racon {      cpus = params.cores } 
+    withLabel: medaka {     cpus = params.cores }
     withLabel: pilon {      cpus = params.cores; memory = params.memory }
     withLabel: ubuntu {     cpus = 1 } 
     withLabel: kmc {        cpus = params.cores } 
+    withLabel: khmer {      cpus = params.cores } 
 }
diff --git a/configs/node.config b/configs/node.config
@@ -1,20 +1,19 @@
-process {   
-        withLabel: basics {     cpus = 2 ;  memory = '16 GB' }
-        withLabel: bbmap {      cpus = 24 ; memory = '16 GB' }
-        withLabel: bwa {        cpus = 12 ;  memory = '8 GB' }
-        withLabel: fastp {      cpus = 12 ; memory = '16 GB' }
-        withLabel: prodigal {   cpus = 1 ;  memory = '4 GB' }
-        withLabel: diamond {    cpus = 24 ; memory = '16 GB' }
-        withLabel: ggplot2 {    cpus = 2 ;  memory = '4 GB' }
-        withLabel: nanoplot {   cpus = 8 ;  memory = '14 GB' }
-        withLabel: spades {     cpus = 32 ; memory = '80 GB' }
-        withLabel: sourmash {   cpus = 8 ;  memory = '24 GB' }
-        withLabel: flye {       cpus = 12 ; memory = '80 GB' }
-        withLabel: minimap2 {   cpus = 8 ;  memory = '24 GB' }
-        withLabel: racon {      cpus = 4 ;  memory = '4 GB' }  
-        withLabel: samtools {   cpus = 8 ;  memory = '8 GB' }  
-        withLabel: medaka {     cpus = 20 ; memory = '40 GB' }
-        withLabel: pilon {      cpus = 20 ; memory = '40 GB' } 
-        withLabel: ubuntu {     cpus = 4 ;  memory = '8 GB' } 
-        withLabel: kmc {        cpus = 8 ;  memory = '16 GB' } 
+process {
+    withLabel: basics   { cpus = 1; memory = 2.GB }
+    withLabel: bbmap    { cpus = 16; memory = 24.GB }
+    withLabel: prodigal { cpus = 8 ; memory = 16.GB }
+    withLabel: diamond  { cpus = 12 ; memory = 16.GB }
+    withLabel: ggplot2  { cpus = 2 ; memory = 4.GB }
+    withLabel: ubuntu   { cpus = 1; memory = 2.GB }
+    withLabel: fastp    { cpus = 12; memory = 8.GB }
+    withLabel: nanoplot { cpus = 4; memory = 8.GB; }
+    withLabel: spades   { cpus = 24; memory = 60.GB }
+    withLabel: flye     { cpus = {24 * task.attempt}; memory = {60.GB * task.attempt}; errorStrategy = { task.exitStatus in 1 || 130..140 ? 'retry' : 'terminate' }; maxRetries = 2; }
+    withLabel: minimap2 { cpus = 8; memory = 24.GB }
+    withLabel: racon    { cpus = 16; memory = 36.GB }
+    withLabel: medaka   { cpus = 16; memory = 24.GB }
+    withLabel: pilon    { cpus = 20 ; memory = 40 } 
+    withLabel: kmc      { cpus = 8; memory = 16.GB }
 }
+
+// LSF: ; clusterOptions = '-P bigmem'
diff --git a/envs/flye.yaml b/envs/flye.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - flye=2.8
+  - flye=2.9.3
diff --git a/envs/medaka.yaml b/envs/medaka.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - medaka=1.0.3
+  - medaka=1.11.3
diff --git a/envs/minimap2.yaml b/envs/minimap2.yaml
@@ -3,5 +3,5 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - minimap2=2.17
-  - samtools=1.9
+  - minimap2=2.26
+  - samtools=1.19.2
diff --git a/envs/nanoplot.yaml b/envs/nanoplot.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - nanoplot=1.32.0
+  - nanoplot=1.25.0
diff --git a/envs/racon.yaml b/envs/racon.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - racon=1.4.13
+  - racon=1.5.0
diff --git a/envs/samtools.yaml b/envs/samtools.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - conda-forge
 dependencies:
-  - samtools=1.10
+  - samtools=1.19.2