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updated docker images for mapping_patlas and mash_screen #131

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Merged
merged 2 commits into from
Sep 25, 2018
Merged

updated docker images for mapping_patlas and mash_screen #131

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3cbef2c
updated docker images for mapping_patlas and mash_screen
tiagofilipe12 Sep 25, 2018
1eba5f3
updated changelog
tiagofilipe12 Sep 25, 2018
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7 changes: 7 additions & 0 deletions changelog.md
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@@ -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
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6 changes: 3 additions & 3 deletions docs/user/components/mapping_patlas.rst
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Expand Up @@ -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
4 changes: 2 additions & 2 deletions docs/user/components/mash_dist.rst
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Expand Up @@ -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
4 changes: 2 additions & 2 deletions docs/user/components/mash_screen.rst
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Expand Up @@ -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
4 changes: 2 additions & 2 deletions flowcraft/generator/components/distance_estimation.py
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Expand Up @@ -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'"
}
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4 changes: 2 additions & 2 deletions flowcraft/generator/components/patlas_mapping.py
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Expand Up @@ -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'"
}
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2 changes: 1 addition & 1 deletion flowcraft/generator/templates/mapping_patlas.nf
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion flowcraft/generator/templates/mash_dist.nf
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Expand Up @@ -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 }}
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