README.md 6.57 KB
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[//]: # "#to make links in gitlab: example with racon https://github.com/isovic/racon"
[//]: # "tricks in markdown: https://openclassrooms.com/fr/courses/1304236-redigez-en-markdown"

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[![Nextflow](https://img.shields.io/badge/code-Nextflow-blue?style=plastic)](https://www.nextflow.io/)
 
[![License: GPL-3.0](https://img.shields.io/badge/licence-GPL%20(%3E%3D3)-green?style=plastic)](https://www.gnu.org/licenses)

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## TABLE OF CONTENTS


   - [AIM](#aim)
   - [CONTENT](#content)
   - [HOW TO RUN](#how-to-run)
   - [OUTPUT](#output)
   - [VERSIONS](#versions)
   - [LICENCE](#licence)
   - [CITATION](#citation)
   - [CREDITS](#credits)
   - [ACKNOWLEDGEMENTS](#Acknowledgements)
   - [WHAT'S NEW IN](#what's-new-in)


## AIM




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## CONTENT

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**main.nf** file that can be executed using a CLI (command line interface)

**nextflow.config** parameter settings for the main.nf file

**dataset** folder containing some datasets than can be used as examples

test.fastq.gz: first 4,000 lines of Pool-B2699_S1_L001_R1_001.fastq.gz from /pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/dataset/B2699/00_Rawdata/Pool-B2699_S1_L001_R1_001.fastq.gz

primer_fasta: from /pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot/results/20200520_res_CL14985_newtrim_align/20200520_adapters_TruSeq_B2699_14985_CL.fasta

**example_of_result** folder containing an example of result obtained with the dataset

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## HOW TO RUN

See Protocol 136 (ask me).


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### If error message
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If an error message appears, like:
```
Unknown error accessing project `gmillot/14985_loot` -- Repository may be corrupted: /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot/14985_loot
```
Purge using:
```
rm -rf /pasteur/sonic/homes/gmillot/.nextflow/assets/gmillot*
```


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### Using the committed version on gitlab:

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1) Create the scm file:
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```bash
providers {
    pasteur {
        server = 'https://gitlab.pasteur.fr'
        platform = 'gitlab'
    }
}
```

And save it as 'scm' in the .nextflow folder. For instance in:
\\wsl$\Ubuntu-20.04\home\gael\.nextflow

Warning: ssh key must be set for gitlab, to be able to use this procedure (see protocol 44).

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2) Mount a server if required:
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```bash
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DRIVE="C"
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sudo mkdir /mnt/share
sudo mount -t drvfs $DRIVE: /mnt/share
```

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Warning: if no mounting, it is possible that nextflow does nothing, or displays a message like
```
Launching `main.nf` [loving_morse] - revision: d5aabe528b
/mnt/share/Users
```

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3) Then run the following command from here \\wsl$\Ubuntu-20.04\home\gael:
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```bash
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nextflow run -hub pasteur gmillot/08002_bourgeron -r v1.0.0
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```

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If an error message appears, like:
```
WARN: Cannot read project manifest -- Cause: Remote resource not found: https://gitlab.pasteur.fr/api/v4/projects/gmillot%2F08002_bourgeron
```
Make the distant repo public

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If an error message appears, like:

```
permission denied
```

See chmod in protocol 44.

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### Using a cluster

Start with:

```bash
EXEC_PATH="/pasteur/zeus/projets/p01/BioIT/gmillot/14985_loot" # where the bin folder of the main.nf script is located
export CONF_BEFORE=/opt/gensoft/exe # on maestro

export JAVA_CONF=java/13.0.2
export JAVA_CONF_AFTER=bin/java # on maestro
export SINGU_CONF=singularity/3.8.3
export SINGU_CONF_AFTER=bin/singularity # on maestro
export GIT_CONF=git/2.25.0
export GIT_CONF_AFTER=bin/git # on maestro
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export GRAPHVIZ_CONF=graphviz/2.42.3
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export GRAPHVIZ_CONF_AFTER=bin/graphviz # on maestro
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MODULES="${CONF_BEFORE}/${JAVA_CONF}/${JAVA_CONF_AFTER},${CONF_BEFORE}/${SINGU_CONF}/${SINGU_CONF_AFTER},${CONF_BEFORE}/${GIT_CONF}/${GIT_CONF_AFTER},${CONF_BEFORE}/${GRAPHVIZ_CONF}/${GRAPHVIZ_CONF_AFTER}"
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# cd ${EXEC_PATH} # not required when using the gitlab repo to run the script
# chmod 755 ${EXEC_PATH}/bin/*.* # not required when using the gitlab repo to run the script
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module load ${JAVA_CONF} ${SINGU_CONF} ${GIT_CONF} ${GRAPHVIZ_CONF}
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```

Then run:

```bash
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# distant main.nf file
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HOME="$ZEUSHOME/14985_loot/" ; nextflow run --modules ${MODULES} -hub pasteur gmillot/14985_loot -r v7.6.0 ; HOME="/pasteur/appa/homes/gmillot/"
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# local main.nf file ($HOME changed to allow the creation of .nextflow into /$ZEUSHOME/14985_loot/. See NFX_HOME in the nextflow soft script)
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HOME="$ZEUSHOME/14985_loot/" ; nextflow run --modules ${MODULES} main.nf ; HOME="/pasteur/appa/homes/gmillot/"
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```


## OUTPUT




## VERSIONS


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The different releases are tagged [here](https://gitlab.pasteur.fr/gmillot/14985_loot/-/tags)
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## LICENCE


This package of scripts can be redistributed and/or modified under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
Distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchandability or fitness for a particular purpose.
See the GNU General Public License for more details at https://www.gnu.org/licenses.


## CITATION


Not yet published


## CREDITS


[Gael A. Millot](https://gitlab.pasteur.fr/gmillot), Hub-CBD, Institut Pasteur, Paris, France


## ACKNOWLEDGEMENTS


Frédéric Lemoine, Hub-CBD, Institut Pasteur, Paris

Bertrand Néron, Hub-CBD, Institut Pasteur, Paris

The mentioned softwares and packages developers & maintainers

Gitlab developers


## WHAT'S NEW IN

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### v7.7.0

1) Kraken added and multiQC fixed


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### v7.6.0

1) Everything's fine, except the multiQC


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### v7.5.0

1) Ok up to the plot_insertion process, tested using the test file


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### v7.4.0

1) Ok up to global logo, tested using the test file


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### v7.3.0

1) flow and files improved by Fred, because of the relative paths, no need of dev/


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### v7.2.0

1) better priority for slurm


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### v7.1.0

1) dev/test.config adapted to slurm

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### v7.0.0

1) Ok up to insertion freq, tested using the test file


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### v6.1.0

1) config file debugged


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### v6.0.0

1) Ok up to q20 tested using the test file


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### v5.1.0

1) html report improved a bit


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### v5.0.0

1) Now the results are compiled in a html report


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### v4.1.0

1) Ok up to plot after attC read selection and attC trimming, tested on full B2699, and debugged

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### v4.0.0

1) Ok up to plot after attC read selection and attC trimming, tested on full B2699


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### v3.1.0

1) report improved


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### v3.0.0

1) Ok up to plot after attC read selection and attC trimming

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### v2.0.0

1) Ok up to fastq files QC


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### v1.0.0

1) Backbone for nextflow scripts and config files