doc/img/webide.png.license

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

doc/mail.txt

@@ -19,3 +19,24 @@ If you want to work on your laptop, or plan to work remotely on your desktop via
 - docker
 
 Best,
+
+Dear all,
+
+You registered to the formation Git (12/12) or/and the formation Nextlflow (13/12) from 13:30 pm to 18pm in the in the room M7.1H04.
+
+Please check that you have an account on our gitlab server at the following url : 
+https://gitlab.biologie.ens-lyon.fr (only available from the ENS network)
+To connect, simply click on the CAS button.
+Your account is now linked to the gitlab server, but blocked
+You can send an email to laurent.modolo@ens-lyon.fr to activate your account.
+
+You will also need an account on the PSMN (http://www.ens-lyon.fr/PSMN/doku.php?id=contact:forms:inscription) (don’t wait until the 12 to request an account !)
+
+If you want to work on your laptop, or plan to work remotely on your desktop via ssh (http://www.ens-lyon.fr/LBMC/intranet/services-communs/pole-bioinformatique/bioinfo_club/1_ssh_and_other_tools_to_work_remotly) you need to have the following software installed :
+- ssh
+- git
+- java (>=1.8) (for the nextflow formation)
+- docker (for the nextflow formation)
+Otherwise, you will need to request an account to use the computer in the room (http://www.cbp.ens-lyon.fr/doku.php?id=contact:compte)
+
+Best,

doc/mail.txt.license

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

doc/nf_projects.md

+<!--
+SPDX-FileCopyrightText: 2022 Laurent Modolo <laurent.modolo@ens-lyon.fr>
+
+SPDX-License-Identifier: CC-BY-SA-4.0
+-->
+
 ## Projects using nextflow
 
+This page list existing Nextflow based pipeline projects into different categories
+
+- [RNASeq](./nf_projects.md#rnaseq)
+- [scRNASeq](./nf_projects.m#scrnaseq)
+- [DNASeq](./nf_projects.md#dnaseq)
+- [ChipSeq](./nf_projects.md#chipseq)
+
+To add your project to this list, please fork this project, modify this file and make a merge request.
+![merge request button](./img/merge_request.png)
+
 ### RNASeq
 
 - [https://_https://gitlab.biologie.ens-lyon.fr/gylab/salmoninyeast](https://_https://gitlab.biologie.ens-lyon.fr/gylab/salmoninyeast)
 - [https://github.com/LBMC/readthroughpombe](https://github.com/LBMC/readthroughpombe)
 - [https://_https://gitlab.biologie.ens-lyon.fr/vvanoost/nextflow](https://_https://gitlab.biologie.ens-lyon.fr/vvanoost/nextflow)
+- [https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project](https://gitlab.biologie.ens-lyon.fr/elabaron/HIV_project)  
+- [https://gitbio.ens-lyon.fr/LBMC/Palladino/RNAseq_nextflow](https://gitbio.ens-lyon.fr/LBMC/Palladino/RNAseq_nextflow)
 
-### single-cell RNA_-Seq
+### scRNASeq
 
 - [https://gitlab.com/LBMC_UMR5239/sbdm/mars-seq](https://gitlab.com/LBMC_UMR5239/sbdm/mars-seq)
 
 ### DNASeq
 
 - [https://github.com/LBMC/ChrSexebelari](https://github.com/LBMC/ChrSexebelari)
+- [https://gitbio.ens-lyon.fr/LBMC/gylab/MappingNoise](https://gitbio.ens-lyon.fr/LBMC/gylab/MappingNoise)
+- [https://gitbio.ens-lyon.fr/LBMC/qrg/droso_hic_group/droso_haplo_rna_seq](https://gitbio.ens-lyon.fr/LBMC/qrg/droso_hic_group/droso_haplo_rna_seq)
 
 ### Chip-Seq
 
 - [https://gitlab.biologie.ens-lyon.fr/Auboeuf/ChIP-seq](https://gitlab.biologie.ens-lyon.fr/Auboeuf/ChIP-seq)
+- [https://gitbio.ens-lyon.fr/LBMC/Bernard/quantitative-nucleosome-analysis](https://gitbio.ens-lyon.fr/LBMC/Bernard/quantitative-nucleosome-analysis)
 

results/.gitignore

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

src/.conda_envs/.conda_envs_dir_test

-/Xnfs/lbmcdb/common/conda/envs/.conda_envs_dir_test
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src/.conda_envs/Python_2.7.13

-/Xnfs/lbmcdb/common/conda/envs/Python_2.7.13
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src/.conda_envs/Python_3.6.1

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src/.conda_envs/R_3.3.1

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src/.conda_envs/R_3.4.3

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src/.conda_envs/axtchain_377

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src/.conda_envs/bcftools_1.7

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src/.conda_envs/bedtools_2.25.0

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src/.conda_envs/bioawk_1.0

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src/.conda_envs/biopython_1.74

-/Xnfs/lbmcdb/common/conda/envs/biopython_1.74
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src/.conda_envs/bowtie2_2.3.2

-/Xnfs/lbmcdb/common/conda/envs/bowtie2_2.3.2
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src/.conda_envs/bowtie2_2.3.4.1

-/Xnfs/lbmcdb/common/conda/envs/bowtie2_2.3.4.1
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src/.conda_envs/canu_1.7

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