Merge branch nextflow:master into master

src/.docker_modules/cellphonedb/3.0.0/requirements-web.txt.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

src/.docker_modules/cellphonedb/3.0.0/requirements.txt

+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

src/.docker_modules/cellphonedb/3.0.0/requirements.txt.license

+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0

src/.docker_modules/clustalo/1.2.4/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+FROM debian:stretch-slim
+
+ENV CLUSTALO_VERSION=1.2.4-1
+ENV PACKAGES clustalo=${CLUSTALO_VERSION} \
+  procps 
+
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends ${PACKAGES} && \
+    apt-get clean

src/.docker_modules/clustalo/1.2.4/docker_init.sh

+#!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
+docker pull lbmc/clustalo:1.2.4
+# docker build src/.docker_modules/clustalo/1.2.4 -t 'lbmc/clustalo:1.2.4'
+# docker push lbmc/clustalo:1.2.4
+docker buildx build --platform linux/amd64,linux/arm64 -t "lbmc/clustalo:1.2.4" --push src/.docker_modules/clustalo/1.2.4

src/.docker_modules/crossmap/0.4.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM quay.io/biocontainers/crossmap:0.4.1--pyh5ca1d4c_0
 MAINTAINER Laurent Modolo

src/.docker_modules/crossmap/0.4.1/docker_init.sh

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 docker pull lbmc/crossmap:0.4.1
 # docker build src/.docker_modules/crossmap/0.4.1/ -t 'lbmc/crossmap:0.4.1'
 # docker push lbmc/crossmap:0.4.1

src/.docker_modules/cutadapt/1.14/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM alpine:3.8
 MAINTAINER Laurent Modolo
 

src/.docker_modules/cutadapt/1.14/docker_init.sh

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 docker pull lbmc/cutadapt:1.14
 # docker build src/.docker_modules/cutadapt/1.14 -t 'lbmc/cutadapt:1.14'
 # docker push lbmc/cutadapt:1.14

src/.docker_modules/cutadapt/1.15/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM alpine:3.8
 MAINTAINER Laurent Modolo
 

src/.docker_modules/cutadapt/1.15/docker_init.sh

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 docker pull lbmc/cutadapt:1.15
 # docker build src/.docker_modules/cutadapt/1.15 -t 'lbmc/cutadapt:1.15'
 # docker push lbmc/cutadapt:1.15

src/.docker_modules/cutadapt/2.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM alpine:3.8
 MAINTAINER Laurent Modolo
 

src/.docker_modules/cutadapt/2.1/docker_init.sh

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 docker pull lbmc/cutadapt:2.1
 # docker build src/.docker_modules/cutadapt/2.1 -t 'lbmc/cutadapt:2.1'
 # docker push lbmc/cutadapt:2.1

src/.docker_modules/danpos3/2f7f223/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM ubuntu:20.04 
 
 ENV DANPOS_VERSION="2f7f223"

src/.docker_modules/danpos3/2f7f223/docker_init.sh

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 docker pull lbmc/danpos3:2f7f223
 # docker build src/.docker_modules/danpos3/2f7f223 -t 'lbmc/danpos3:2f7f223'
 # docker push lbmc/danpos3:2f7f223

src/.docker_modules/deeptools/3.0.2/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM debian:stretch
 MAINTAINER Laurent Modolo
 

src/.docker_modules/deeptools/3.0.2/docker_init.sh

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 docker pull lbmc/deeptools:3.0.2
 # docker build src/.docker_modules/deeptools/3.0.2 -t 'lbmc/deeptools:3.0.2'
 # docker push lbmc/deeptools:3.0.2

src/.docker_modules/deeptools/3.1.1/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM debian:stretch
 MAINTAINER Laurent Modolo
 

src/.docker_modules/deeptools/3.1.1/docker_init.sh

 #!/bin/sh
+
+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 docker pull lbmc/deeptools:3.1.1
 # docker build src/.docker_modules/deeptools/3.1.1 -t 'lbmc/deeptools:3.1.1'
 # docker push lbmc/deeptools:3.1.1

src/.docker_modules/deeptools/3.5.0/Dockerfile

+# SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+#
+# SPDX-License-Identifier: AGPL-3.0-or-later
+
 FROM python:3.9-slim
 MAINTAINER Lauret Modolo