From e2454d73c29dc6cfe808a5bc580bb2fb2b2d4d77 Mon Sep 17 00:00:00 2001
From: Laurent Modolo <laurent.modolo@ens-lyon.fr>
Date: Thu, 24 Feb 2022 09:49:53 +0100
Subject: [PATCH] Close merge request #27

---
 .../bedtools/2.30.0/docker_init.sh            |   5 +-
 .../cellphonedb/3.0.0/Dockerfile              |  21 ++++
 .../cellphonedb/3.0.0/cellphonedb.ini         |  14 +++
 .../3.0.0/docker/postgres/Dockerfile          |   5 +
 .../cellphonedb/3.0.0/docker/run-system.sh    |   3 +
 .../cellphonedb/3.0.0/requirements-web.txt    |   6 +
 .../cellphonedb/3.0.0/requirements.txt        |  18 +++
 .../htseq/0.13.5/docker_init.sh               |   5 +-
 src/.docker_modules/kb/0.26.3/docker_init.sh  |   5 +-
 src/.docker_modules/sanity/Dockerfile         |  30 +++++
 src/.docker_modules/sanity/docker_init.sh     |   4 +
 src/nf_modules/cellphonedb/main.nf            | 118 ++++++++++++++++++
 src/nf_modules/fastp/main.nf                  |   1 +
 src/nf_modules/kb/main.nf                     |   2 +-
 src/nf_modules/sanity/main.nf                 |  35 ++++++
 15 files changed, 262 insertions(+), 10 deletions(-)
 create mode 100644 src/.docker_modules/cellphonedb/3.0.0/Dockerfile
 create mode 100644 src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini
 create mode 100644 src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile
 create mode 100755 src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh
 create mode 100644 src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt
 create mode 100644 src/.docker_modules/cellphonedb/3.0.0/requirements.txt
 create mode 100644 src/.docker_modules/sanity/Dockerfile
 create mode 100755 src/.docker_modules/sanity/docker_init.sh
 create mode 100644 src/nf_modules/cellphonedb/main.nf
 create mode 100644 src/nf_modules/sanity/main.nf

diff --git a/src/.docker_modules/bedtools/2.30.0/docker_init.sh b/src/.docker_modules/bedtools/2.30.0/docker_init.sh
index fa7f1fde..b23fa27e 100755
--- a/src/.docker_modules/bedtools/2.30.0/docker_init.sh
+++ b/src/.docker_modules/bedtools/2.30.0/docker_init.sh
@@ -1,5 +1,4 @@
 #!/bin/sh
 docker pull lbmc/bedtools:2.30.0
-# docker build src/.docker_modules/bedtools/2.30.0 -t 'lbmc/bedtools:2.30.0'
-# docker push lbmc/bedtools:2.30.0
-docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/bedtools:2.30.0" --push src/.docker_modules/bedtools/2.30.0
+docker build src/.docker_modules/bedtools/2.30.0 -t 'lbmc/bedtools:2.30.0'
+docker push lbmc/bedtools:2.30.0
diff --git a/src/.docker_modules/cellphonedb/3.0.0/Dockerfile b/src/.docker_modules/cellphonedb/3.0.0/Dockerfile
new file mode 100644
index 00000000..18e7cf71
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/Dockerfile
@@ -0,0 +1,21 @@
+FROM python:3.7-slim 
+
+ENV RPY2_CFFI_MODE=ABI
+
+RUN mkdir /app /docker
+COPY requirements.txt /app
+COPY requirements-web.txt /app
+WORKDIR /app
+
+RUN pip install -r requirements.txt
+RUN pip install -r requirements-web.txt
+RUN pip install cellphonedb==3.0.0
+
+
+COPY . /app
+COPY ./docker /docker
+RUN mkdir -p /var/log/uwsgi
+RUN touch /var/log/uwsgi/cellphonedb.log
+RUN chmod +x /app
+
+CMD ["/docker/run-system.sh"]
diff --git a/src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini b/src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini
new file mode 100644
index 00000000..ea75bcab
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/cellphonedb.ini
@@ -0,0 +1,14 @@
+[uwsgi]
+module = wsgi:app
+
+master = true
+processes = 4
+
+
+socket = 0.0.0.0:5000
+chmod-socket = 660
+vacuum = true
+
+die-on-term = true
+
+stats = /tmp/stats.socket
\ No newline at end of file
diff --git a/src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile b/src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile
new file mode 100644
index 00000000..25b936ad
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/docker/postgres/Dockerfile
@@ -0,0 +1,5 @@
+FROM postgres:9.6
+
+ENV POSTGRES_PASSWORD  root
+ENV POSTGRES_USER root
+ENV POSTGRES_DB cellphonedb
\ No newline at end of file
diff --git a/src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh b/src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh
new file mode 100755
index 00000000..9b8cd443
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/docker/run-system.sh
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+exec uwsgi --ini cellphonedb.ini --log-master
diff --git a/src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt b/src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt
new file mode 100644
index 00000000..fa15fd0b
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt
@@ -0,0 +1,6 @@
+flask>=1.1,<1.1.99
+Flask-RESTful>=0.3,<0.3.99
+Flask-Testing>=0.8,<0.8.99
+pika>=0.12,<0.12.99
+boto3>=1.7,<1.7.99
+uWSGI>=2.0,<2.0.99
diff --git a/src/.docker_modules/cellphonedb/3.0.0/requirements.txt b/src/.docker_modules/cellphonedb/3.0.0/requirements.txt
new file mode 100644
index 00000000..2f7e9961
--- /dev/null
+++ b/src/.docker_modules/cellphonedb/3.0.0/requirements.txt
@@ -0,0 +1,18 @@
+click>=7.0,<8.0
+pandas>=1.0.0,<=1.1.4
+numpy>=1.16.5,<=1.19.5
+numpy-groupies
+scikit-learn==0.22
+flask>=1.0,<2.0.0
+Flask-RESTful>=0.3
+Flask-Testing>=0.7
+SQLAlchemy>=1.3,<1.4
+PyYAML>=5.4,<6.0
+requests>=2.25,<3.0
+pika>=1.0.0,<2.0
+boto3>=1.15,<2.0
+geosketch==0.3
+rpy2>=3.4.0,<4.0
+tqdm>=4.3,<5.0
+h5py<3.0.0
+anndata>=0.7,<=0.75
diff --git a/src/.docker_modules/htseq/0.13.5/docker_init.sh b/src/.docker_modules/htseq/0.13.5/docker_init.sh
index 00ad38fe..ca03fe9a 100755
--- a/src/.docker_modules/htseq/0.13.5/docker_init.sh
+++ b/src/.docker_modules/htseq/0.13.5/docker_init.sh
@@ -1,5 +1,4 @@
 #!/bin/sh
 docker pull lbmc/htseq:0.13.5
-# docker build src/.docker_modules/htseq/0.13.5 -t 'lbmc/htseq:0.13.5'
-# docker push lbmc/htseq:0.13.5
-docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/htseq:0.13.5" --push src/.docker_modules/htseq/0.13.5
+docker build src/.docker_modules/htseq/0.13.5 -t 'lbmc/htseq:0.13.5'
+docker push lbmc/htseq:0.13.5
diff --git a/src/.docker_modules/kb/0.26.3/docker_init.sh b/src/.docker_modules/kb/0.26.3/docker_init.sh
index 8104fc75..0294274a 100755
--- a/src/.docker_modules/kb/0.26.3/docker_init.sh
+++ b/src/.docker_modules/kb/0.26.3/docker_init.sh
@@ -1,5 +1,4 @@
 #!/bin/sh
 docker pull lbmc/kb:0.26.3
-# docker build src/.docker_modules/kb/0.26.3 -t 'lbmc/kb:0.26.3'
-# docker push lbmc/kb:0.26.3
-docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/kb:0.26.3" --push src/.docker_modules/kb/0.26.3
+docker build src/.docker_modules/kb/0.26.3 -t 'lbmc/kb:0.26.3'
+docker push lbmc/kb:0.26.3
diff --git a/src/.docker_modules/sanity/Dockerfile b/src/.docker_modules/sanity/Dockerfile
new file mode 100644
index 00000000..99f9545e
--- /dev/null
+++ b/src/.docker_modules/sanity/Dockerfile
@@ -0,0 +1,30 @@
+##### BASE IMAGE #####
+FROM ubuntu:18.04
+
+##### METADATA #####
+LABEL base.image="ubuntu:18.04"
+LABEL version="1"
+LABEL software="Sanity"
+LABEL software.version="1.0"
+LABEL software.description="Sanity"
+LABEL software.website=""
+LABEL software.documentation="https://github.com/jmbreda/Sanity"
+
+##### VARIABLES #####
+
+# Use variables for convenient updates/re-usability
+ENV SOFTWARE_VERSION 1.0
+
+RUN apt-get update \
+  && apt-get install -y tzdata \
+  && ln -fs /usr/share/zoneinfo/Europe/Berlin /etc/localtime \
+  && dpkg-reconfigure --frontend noninteractive tzdata \
+  && apt-get install --yes git make g++ libgomp1 \
+  && git clone https://github.com/jmbreda/Sanity.git \
+  && cd Sanity \
+  && cd src \
+  && make \
+  && cp ../bin/Sanity /usr/bin \
+  && cd ../../ \
+  && rm -rf Sanity \
+  && apt-get remove --purge --yes git make g++ \
diff --git a/src/.docker_modules/sanity/docker_init.sh b/src/.docker_modules/sanity/docker_init.sh
new file mode 100755
index 00000000..876fecd8
--- /dev/null
+++ b/src/.docker_modules/sanity/docker_init.sh
@@ -0,0 +1,4 @@
+#!/bin/sh
+docker pull mlepetit/saanity
+docker build src/.docker_modules/mlepetit/sanity -t 'lbmc/sanity'
+docker push lbmc/sanity
diff --git a/src/nf_modules/cellphonedb/main.nf b/src/nf_modules/cellphonedb/main.nf
new file mode 100644
index 00000000..37fb9700
--- /dev/null
+++ b/src/nf_modules/cellphonedb/main.nf
@@ -0,0 +1,118 @@
+version = "3.0.0"
+container_url = "mlepetit/cellphonedb:latest"
+
+params.cellphonedb = ""
+params.cellphonedb_out = ""
+params.pval=""
+params.thres=""
+params.iterations=""
+params.gene_id=""
+
+
+
+workflow cellphone_statistical_analysis {
+  take:
+    meta
+    counts
+
+  main:
+
+cpdb_methods_stats(meta,counts)
+cpdb_plot_dot_plot(cpdb_methods_stats.out.means,cpdb_methods_stats.out.pvalues)
+cpdb_plot_heatmap(cpdb_methods_stats.out.pvalues)
+
+
+  emit:
+    means = cpdb_methods_stats.out.means
+    pvalues = cpdb_methods_stats.out.pvalues
+    deconvoluted = cpdb_methods_stats.out.deconvoluted
+    significant_means = cpdb_methods_stats.out.significant_means
+    dot_plot = cpdb_plot_dot_plot.out.dot_plot
+    heatmap = cpdb_plot_heatmap.out.heatmap
+    heatmap_log = cpdb_plot_heatmap.out.heatmap_log
+    count_network = cpdb_plot_heatmap.out.count_network
+    interactions_count = cpdb_plot_heatmap.out.interactions_count
+
+
+}
+
+
+
+
+
+
+
+
+
+
+process cpdb_methods_stats {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+    if (params.cellphonedb_out != "") {
+    publishDir "results/${params.cellphonedb_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(id_mtx), path(meta)
+    tuple val(id_mtx), path(counts)
+  
+  output:
+   tuple val(id_mtx), path("out/means.txt"), emit: means
+   tuple val(id_mtx), path("out/pvalues.txt"), emit: pvalues
+   tuple val(id_mtx), path("out/deconvoluted.txt"), emit: deconvoluted
+   tuple val(id_mtx), path("out/significant_means.txt"), emit: significant_means
+  
+script:
+  """
+cellphonedb method statistical_analysis ${params.meta} ${params.counts} --counts-data ${params.gene_id}  --threads ${task.cpus} --iterations ${params.iterations} --pvalue ${params.pval} --threshold ${params.thres}
+
+  """
+}
+
+
+process cpdb_plot_dot_plot {
+  container = "${container_url}"
+  label "big_mem_mono_cpus"
+    if (params.cellphonedb_out != "") {
+    publishDir "results/${params.cellphonedb_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(id_mtx), path(means)
+    tuple val(id_mtx), path(pvalues)
+
+  output:
+   tuple val(id_mtx), path("out/plot.pdf"), emit: dot_plot
+
+script:
+  """
+mkdir ./out
+cellphonedb plot dot_plot --means-path ${means} --pvalues-path ${pvalues} 
+
+  """
+}
+ 
+process cpdb_plot_heatmap {
+  container = "${container_url}"
+  label "big_mem_multi_cpus"
+    if (params.cellphonedb_out != "") {
+    publishDir "results/${params.cellphonedb_out}", mode: 'copy'
+  }
+
+  input:
+    tuple val(id_mtx), path(pvalues)
+
+  output:
+   tuple val(id_mtx), path("out/heatmap_count.pdf"), emit: heatmap
+ tuple val(id_mtx), path("out/heatmap_log_count.pdf"), emit: heatmap_log
+ tuple val(id_mtx), path("out/count_network.txt"), emit: count_network
+ tuple val(id_mtx), path("out/interaction_count.txt"), emit: interactions_count
+
+script:
+ 
+ """
+mkdir ./out
+cellphonedb plot heatmap_plot --pvalues-path ${pvalues} --pvalue ${params.pval} ${params.meta}
+
+  """
+}
diff --git a/src/nf_modules/fastp/main.nf b/src/nf_modules/fastp/main.nf
index 2593eefe..92ee81fc 100644
--- a/src/nf_modules/fastp/main.nf
+++ b/src/nf_modules/fastp/main.nf
@@ -151,3 +151,4 @@ process fastp_accel_1splus {
       --report_title ${file_prefix}
   """
 }
+
diff --git a/src/nf_modules/kb/main.nf b/src/nf_modules/kb/main.nf
index ca4e7552..6edfa130 100644
--- a/src/nf_modules/kb/main.nf
+++ b/src/nf_modules/kb/main.nf
@@ -268,7 +268,7 @@ workflow index_fasta_velocity {
 
 process index_fasta_velocity_default {
   container = "${container_url}"
-  label "big_mem_mono_cpus"
+  label "big_mem_multi_cpus"
   tag "$file_id"
   if (params.index_fasta_out != "") {
     publishDir "results/${params.index_fasta_out}", mode: 'copy'
diff --git a/src/nf_modules/sanity/main.nf b/src/nf_modules/sanity/main.nf
new file mode 100644
index 00000000..7d9d6236
--- /dev/null
+++ b/src/nf_modules/sanity/main.nf
@@ -0,0 +1,35 @@
+container_url="mlepetit/sanity:latest"
+
+params.sanity_out=""
+params.sanity=""
+
+process normalization_sanity
+        {
+
+        container="${container_url}"
+        label  "big_mem_multi_cpus"
+        if (params.sanity_out != "") {
+		publishDir "results/${params.sanity_out}", mode: 'copy'
+
+	}
+else {
+          publishDir "results/normalize_matrix/", mode: 'copy'
+
+           }
+
+	input:
+
+               tuple val(id_mtx), path(raw_filtered_mtx)   
+               
+
+        output:
+
+               tuple val(id_mtx),path("log_transcription_quotients.txt"), emit: normalize_filtered_mtx
+               tuple val(id_mtx), path("ltq_error_bars.txt")  ,emit: ltq_error
+
+        script:
+
+        """
+        Sanity -f ${raw_filtered_mtx} -n ${task.cpus} ${params.sanity} 
+        """
+        }
-- 
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