updated docker images for mapping_patlas and mash_screen (#131)

* updated docker images for mapping_patlas and mash_screen

* updated changelog

Author: tiagofilipe12

changelog.md

@@ -1,5 +1,12 @@
 # Changelog
 
+## Changes in upcoming release (dev branch) 
+
+### Components changes
+
+Updated images for components `mash_dist`, `mash_screen` and 
+`mapping_patlas`
+
 ## 1.3.0
 
 ### Features

docs/user/components/mapping_patlas.rst

@@ -60,10 +60,10 @@ Default directives
 
 - ``mappingBowtie``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``samtoolsView``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``jsonDumpingMapping``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1

docs/user/components/mash_dist.rst

@@ -65,7 +65,7 @@ Default directives
 
 - ``runMashDist``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``mashDistOutputJson``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1

docs/user/components/mash_screen.rst

@@ -60,7 +60,7 @@ Default directives
 
 - ``mashScreen``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``mashOutputJson``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1

flowcraft/generator/components/distance_estimation.py

@@ -43,13 +43,13 @@ def __init__(self, **kwargs):
         self.directives = {
             "runMashDist": {
                 "container": "flowcraft/mash-patlas",
-                "version": "1.5.2-1",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "{ 4.GB * task.attempt }"
             },
             "mashDistOutputJson": {
                 "container": "flowcraft/mash-patlas",
-                "version": "1.5.2-1",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "'4GB'"
             }

flowcraft/generator/components/patlas_mapping.py

@@ -47,14 +47,14 @@ def __init__(self, **kwargs):
         self.directives = {
             "mappingBowtie": {
                 "container": "flowcraft/mapping-patlas",
-                "version": "1.5.2-2",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "{ 4.GB * task.attempt }",
                 "scratch": "true"
             },
             "jsonDumpingMapping": {
                 "container": "flowcraft/mapping-patlas",
-                "version": "1.5.2-2",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "'4GB'"
             }

flowcraft/generator/templates/mapping_patlas.nf

@@ -57,7 +57,7 @@ process jsonDumpingMapping_{{ pid }} {
 
     tag { sample_id }
 
-    publishDir 'results/mapping/mapping_json_{{ pid }}/', mode: 'copy'
+    publishDir 'results/mapping/mapping_json_{{ pid }}/'
 
     input:
     set sample_id, file(depthFile) from samtoolsResults

flowcraft/generator/templates/mash_dist.nf

@@ -38,7 +38,7 @@ process mashDistOutputJson_{{ pid }} {
 
     tag { sample_id }
 
-    publishDir 'results/mashdist/mashdist_json_{{ pid }}/', mode: 'copy'
+    publishDir 'results/mashdist/mashdist_json_{{ pid }}/'
 
     input:
     set sample_id, fasta, file(mashtxt) from mashDistOutChannel_{{ pid }}