diff --git a/changelog.md b/changelog.md index a63add25..51ab253e 100644 --- a/changelog.md +++ b/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 diff --git a/docs/user/components/mapping_patlas.rst b/docs/user/components/mapping_patlas.rst index 8488a15b..35327b3c 100644 --- a/docs/user/components/mapping_patlas.rst +++ b/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 diff --git a/docs/user/components/mash_dist.rst b/docs/user/components/mash_dist.rst index 7988163d..a47f4207 100644 --- a/docs/user/components/mash_dist.rst +++ b/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 diff --git a/docs/user/components/mash_screen.rst b/docs/user/components/mash_screen.rst index 5d79f38b..c136aa89 100644 --- a/docs/user/components/mash_screen.rst +++ b/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 diff --git a/flowcraft/generator/components/distance_estimation.py b/flowcraft/generator/components/distance_estimation.py index 1bc09de3..3db7bb41 100644 --- a/flowcraft/generator/components/distance_estimation.py +++ b/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'" } diff --git a/flowcraft/generator/components/patlas_mapping.py b/flowcraft/generator/components/patlas_mapping.py index a3eca958..4bd68991 100644 --- a/flowcraft/generator/components/patlas_mapping.py +++ b/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'" } diff --git a/flowcraft/generator/templates/mapping_patlas.nf b/flowcraft/generator/templates/mapping_patlas.nf index 8643fcee..e4245c78 100644 --- a/flowcraft/generator/templates/mapping_patlas.nf +++ b/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 diff --git a/flowcraft/generator/templates/mash_dist.nf b/flowcraft/generator/templates/mash_dist.nf index 13ae560f..50a46ff7 100644 --- a/flowcraft/generator/templates/mash_dist.nf +++ b/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 }}