[scanpy, scrublet] Update scanpy docker image to 1.8.1 and scrublet d…

…ocker image to 0.2.3 Closes #340 Closes #331
vib-singlecell-nf · Jul 8, 2021 · 8370443 · 8370443
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commit 8370443
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Showing 15 changed files with 36 additions and 37 deletions.
diff --git a/conf/test__cell_annotate_filter.config b/conf/test__cell_annotate_filter.config
@@ -16,7 +16,7 @@ params {
             makeVarIndexUnique = false
         }
         scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.0'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
         }
         cell_annotate {
             off = 'h5ad'

diff --git a/conf/test__single_sample_decontx_correct_scrublet.config b/conf/test__single_sample_decontx_correct_scrublet.config
@@ -33,7 +33,7 @@ params {
             }
         }
         scrublet {
-            container = 'vibsinglecellnf/scrublet:0.1.4'
+            container = 'vibsinglecellnf/scrublet:0.2.3'
             labels {
                 processExecutor = 'local'
             }

diff --git a/conf/test__single_sample_scrublet.config b/conf/test__single_sample_scrublet.config
@@ -27,7 +27,7 @@ params {
             }
         }
         scrublet {
-            container = 'vibsinglecellnf/scrublet:0.1.4'
+            container = 'vibsinglecellnf/scrublet:0.2.3'
             labels {
                 processExecutor = 'local'
             }

diff --git a/docs/development.rst b/docs/development.rst
@@ -788,7 +788,7 @@ The parameter structure internally (post-merge) is:
                 }
             }
             scanpy {
-                container = 'docker://vib-singlecell-nf/scanpy:0.5.0'
+                container = 'docker://vib-singlecell-nf/scanpy:1.8.1'
                 filter {
                     ...
                 }

diff --git a/docs/features.rst b/docs/features.rst
@@ -333,7 +333,7 @@ You'll just have to repeat the following structure for the parameters which you
     params {
         sc {
             scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.2'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
             filter {
                 report_ipynb = '/src/scanpy/bin/reports/sc_filter_qc_report.ipynb'
                 // Here we enable the multi-sample feature for the cellFilterMinNgenes parameter
@@ -364,7 +364,7 @@ If you want to apply custom parameters for some specific samples and have a "gen
     params {
         sc {
             scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.2'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
             filter {
                 report_ipynb = '/src/scanpy/bin/reports/sc_filter_qc_report.ipynb'
                 // Here we enable the multi-sample feature for the cellFilterMinNgenes parameter

diff --git a/docs/pipelines.rst b/docs/pipelines.rst
@@ -514,7 +514,7 @@ Make sure the following parts of the generated config are properly set:
     }
     sc {
         scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.2'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
         }
         cell_annotate {
             off = 'h5ad'
@@ -569,7 +569,7 @@ Make sure the following parts of the generated config are properly set:
     }
     sc {
         scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.2'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
         }
         cell_annotate {
             off = 'h5ad'

diff --git a/src/celda/nextflow.config b/src/celda/nextflow.config
@@ -1,7 +1,7 @@
 params {
     sc {
         template {
-            container = 'vibsinglecellnf/scanpy:0.5.0'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
             process1 {
                 param1 = ''
             }

diff --git a/src/scanpy/Dockerfile b/src/scanpy/Dockerfile
@@ -2,9 +2,9 @@ FROM python:3.7.4-slim AS compile-image
 
 ENV DEBIAN_FRONTEND=noninteractive
 RUN BUILDPKGS="build-essential apt-utils \
-        python3-dev libhdf5-dev libfreetype6-dev libtool \
-        m4 autoconf automake patch bison flex libpng-dev libopenblas-dev \
-        tcl-dev tk-dev libxml2-dev zlib1g-dev libffi-dev cmake" && \
+    python3-dev libhdf5-dev libfreetype6-dev libtool \
+    m4 autoconf automake patch bison flex libpng-dev libopenblas-dev \
+    tcl-dev tk-dev libxml2-dev zlib1g-dev libffi-dev cmake" && \
     apt-get update && \
     apt-get install -y --no-install-recommends apt-utils debconf locales && dpkg-reconfigure locales && \
     apt-get install -y --no-install-recommends $BUILDPKGS
@@ -14,23 +14,23 @@ RUN python -m venv /opt/venv
 ENV PATH="/opt/venv/bin:$PATH"
 
 # install dependencies:
-COPY requirements.txt /tmp/
+COPY requirements.txt /tmp/requirements.txt
 RUN pip install --no-cache-dir --upgrade pip && \
     pip install --no-cache-dir -r /tmp/requirements.txt
 
-RUN pip install --no-cache-dir scanpy==1.7.0
+RUN pip install --no-cache-dir scanpy==1.8.1
 
 
 FROM python:3.7.4-slim AS build-image
 
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get -y update && \
     apt-get -y --no-install-recommends install \
-        # Need to run ps
-        procps \
-        libxml2 \
-        # Need to run MulticoreTSNE
-        libgomp1 && \
+    # Need to run ps
+    procps \
+    libxml2 \
+    # Need to run MulticoreTSNE
+    libgomp1 && \
     rm -rf /var/cache/apt/* && \
     rm -rf /var/lib/apt/lists/*
 

diff --git a/src/scanpy/conf/base.config b/src/scanpy/conf/base.config
@@ -1,7 +1,7 @@
 params {
     sc {
         scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.2'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
             report {
                 annotations_to_plot = []
             }

diff --git a/src/scanpy/conf/min.config b/src/scanpy/conf/min.config
@@ -1,7 +1,7 @@
 params {
     sc {
         scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.2'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
             report {
                 annotations_to_plot = []
             }

diff --git a/src/scanpy/requirements.txt b/src/scanpy/requirements.txt
@@ -1,11 +1,11 @@
-anndata==0.7.5
-annoy==1.17.0
+anndata==0.7.6
+annoy==1.15.2
 ansiwrap==0.8.4
 appdirs==1.4.4
 async-generator==1.10
 attrs==20.3.0
 backcall==0.2.0
-bbknn==1.4.0
+bbknn==1.5.1
 beautifulsoup4==4.9.3
 bioservices==1.7.11
 black==20.8b1
@@ -27,7 +27,7 @@ get-version==2.1
 gevent==21.1.2
 greenlet==1.0.0
 grequests==0.6.0
-h5py==3.1.0
+h5py==2.10.0
 idna==2.10
 importlib-metadata==3.4.0
 ipykernel==5.4.3
@@ -46,7 +46,7 @@ leidenalg==0.8.3
 llvmlite==0.35.0
 loompy==3.0.6
 louvain==0.7.0
-lxml==4.6.2
+lxml==4.6.3
 MarkupSafe==1.1.1
 matplotlib==3.3.4
 mistune==0.8.4
@@ -64,10 +64,10 @@ nest-asyncio==1.5.1
 networkx==2.5
 numba==0.52.0
 numexpr==2.7.2
-numpy==1.20.1
+numpy==1.21.0
 numpy-groupies==0.9.13
 packaging==20.9
-pandas==1.2.2
+pandas==1.3.0
 pandocfilters==1.4.3
 papermill==2.3.2
 parso==0.8.1
@@ -91,7 +91,7 @@ pyzmq==22.0.3
 regex==2020.11.13
 requests==2.25.1
 requests-cache==0.5.2
-scikit-learn==0.24.1
+scikit-learn==0.22.0
 scipy==1.6.1
 seaborn==0.11.1
 sinfo==0.3.1
@@ -113,12 +113,12 @@ tqdm==4.57.0
 traitlets==5.0.5
 typed-ast==1.4.2
 typing-extensions==3.7.4.3
-umap-learn==0.5.1
-urllib3==1.26.3
+umap-learn==0.3.10
+urllib3==1.26.5
 wcwidth==0.2.5
 webencodings==0.5.1
 wrapt==1.12.1
 xmltodict==0.12.0
 zipp==3.4.0
 zope.event==4.5.0
-zope.interface==5.2.0
+zope.interface==5.2.0
diff --git a/src/scrublet/Dockerfile b/src/scrublet/Dockerfile
@@ -1,4 +1,3 @@
-FROM vibsinglecellnf/scanpy:0.6.1
+FROM vibsinglecellnf/scanpy:1.8.1
 
 RUN pip install --no-cache-dir scrublet==0.2.3
-
diff --git a/src/scrublet/conf/base.config b/src/scrublet/conf/base.config
@@ -1,7 +1,7 @@
 params {
     sc {
         scrublet {
-            container = 'vibsinglecellnf/scrublet:0.2.1'
+            container = 'vibsinglecellnf/scrublet:0.2.3'
             doublet_detection {
                 report_ipynb = "${params.misc.test.enabled ? '../../..' : ''}/src/scrublet/bin/reports/sc_doublet_detection_report.ipynb"
                 useVariableFeatures = 'False'

diff --git a/src/soupx/nextflow.config b/src/soupx/nextflow.config
@@ -1,7 +1,7 @@
 params {
     sc {
         template {
-            container = 'vibsinglecellnf/scanpy:0.5.0'
+            container = 'vibsinglecellnf/scanpy:1.8.1'
             process1 {
                 param1 = ''
             }

diff --git a/src/utils/conf/test.config b/src/utils/conf/test.config
@@ -1,7 +1,7 @@
 params {
     sc {
         scanpy {
-            container = 'vibsinglecellnf/scanpy:0.5.2'
+            container = 'vibsinglecellnf/scanpy:0.7.0'
         }
         file_converter {
             iff = '10x_cellranger_mex'