Merge branch 'updating_tracks' into 'main'

Updating tracks

See merge request !4

.vscode/extensions.json

@@ -4,6 +4,7 @@
         "visualstudioexptteam.vscodeintellicode",
         "tomoki1207.pdf",
         "christian-kohler.path-intellisense",
-	    "nextflow.nextflow"
+	    "nextflow.nextflow",
+        "janisdd.vscode-edit-csv"
     ]
 }

README.md

 # Jbrowse2 Annelids
 
-
-
-## Getting started
-
-To make it easy for you to get started with GitLab, here's a list of recommended next steps.
-
-Already a pro? Just edit this README.md and make it your own. Want to make it easy? [Use the template at the bottom](#editing-this-readme)!
-
-## Add your files
-
-- [ ] [Create](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#create-a-file) or [upload](https://docs.gitlab.com/ee/user/project/repository/web_editor.html#upload-a-file) files
-- [ ] [Add files using the command line](https://docs.gitlab.com/ee/gitlab-basics/add-file.html#add-a-file-using-the-command-line) or push an existing Git repository with the following command:
-
-```
-cd existing_repo
-git remote add origin https://git.embl.de/grp-arendt/jbrowse2-annelids.git
-git branch -M main
-git push -uf origin main
-```
-
-# Editing this README
-
-When you're ready to make this README your own, just edit this file and use the handy template below (or feel free to structure it however you want - this is just a starting point!). Thanks to [makeareadme.com](https://www.makeareadme.com/) for this template.
-
-## Suggestions for a good README
-
-Every project is different, so consider which of these sections apply to yours. The sections used in the template are suggestions for most open source projects. Also keep in mind that while a README can be too long and detailed, too long is better than too short. If you think your README is too long, consider utilizing another form of documentation rather than cutting out information.
-
-## Name
-Choose a self-explaining name for your project.
-
 ## Description
-Let people know what your project can do specifically. Provide context and add a link to any reference visitors might be unfamiliar with. A list of Features or a Background subsection can also be added here. If there are alternatives to your project, this is a good place to list differentiating factors.
 
-## Badges
-On some READMEs, you may see small images that convey metadata, such as whether or not all the tests are passing for the project. You can use Shields to add some to your README. Many services also have instructions for adding a badge.
+This project intends to manage a Jbrowse2 deployment for annelid genomes in general and *Platynereis dumerilii* in particular.
+
+Jbrowse2 is a genome browser with attractive features, notably that we can add tracks of interest corresponding to variations (VCFs), long read sequencing (GFFs from Pacbio), HI-C, ATACseq runs (BAM).
 
-## Visuals
-Depending on what you are making, it can be a good idea to include screenshots or even a video (you'll frequently see GIFs rather than actual videos). Tools like ttygif can help, but check out Asciinema for a more sophisticated method.
+ The publication reference is [*JBrowse 2: a modular genome browser with views of synteny and structural variation. Genome Biology (2023).*](https://doi.org/10.1186/s13059-023-02914-z)
 
 ## Installation
 Within a particular ecosystem, there may be a common way of installing things, such as using Yarn, NuGet, or Homebrew. However, consider the possibility that whoever is reading your README is a novice and would like more guidance. Listing specific steps helps remove ambiguity and gets people to using your project as quickly as possible. If it only runs in a specific context like a particular programming language version or operating system or has dependencies that have to be installed manually, also add a Requirements subsection.

image/jbrowse_script.sh

@@ -5,3 +5,4 @@ cd annelids
 jbrowse add-assembly https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz --name pdumv021
 jbrowse add-track https://s3.embl.de/annelids/pdumv021/pdumv021.gff.gz -d "Kevin pdumv021 GTF file" -n "Genes models" --category "Annotations"
 jbrowse add-track https://s3.embl.de/annelids/pdumv021/transdecoder.gff.gz -d "Kevin runs transdecoder" -n "Transdecoder results" --category "Annotations"
+jbrowse text-index

resources/genomes.csv

-name,url
-pdumv021,https://s3.embl.de/annelids/pdumv021/pdumv021_genome.fa.gz

resources/variations.csv

-"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN035.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN054.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN055.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN056.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN057.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN058.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN001.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN002.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN003.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN004.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN015.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN016.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN018.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN019.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN020.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN021.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN028.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN029.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN030.vcf"
-"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN031.vcf"

resources_to_s3_NF/README.md

+# Preparing tracks for Jbrowse2
+
+Jbrowse2 typically needs compressed and index files using `bgzip` and `tabix` from `HTSlib` or `SAMtools`.
+This folder contains a Nextflow pipeline that will:
+
+* read CSV files `genomes.csv` and `tracks.csv` to collect the requirements
+* make sure the files are accessible
+* do whatever processing is needed
+* upload it to an EMBL S3 bucket
+* provide a template to populate the `../image/jbrowse_script.sh` file used for Jbrowse2 Docker image
+
+In theory you would have to edit those CSV files, rerun the pipeline and commit the resulting files in order to update Jbrowse2 with new tracks.

resources_to_s3_NF/genomes.csv

+name,path,alias
+pdumv021,/g/arendt/data/genome_assemblies/FINAL_v021_ASM/pdumv021_genome.fa,""
+pmassv1_masked,/g/arendt/data/platynereis_massiliensis/genome/final_assembly/pmassv1.genome.masked.fa,""

resources_to_s3_NF/nextflow.config

+params {
+    config_profile_contact     = "bio-it@embl.de "
+    config_profile_description = "The EMBL Heidelberg HPC cluster profile"
+    config_profile_name        = 'EMBL_HD'
+    config_profile_url         = 'https://git.embl.de/data-sciences/sci-workflows/nextflow-config'
+}
+
+singularity {
+    enabled = true
+    autoMounts = true
+    docker.enabled = false
+    pullTimeout = "3 hours"                // the default is 20 minutes and fails with large images
+    envWhitelist = 'CUDA_VISIBLE_DEVICES'  // allow the bounding of GPU visible device variable into the containers
+}
+
+apptainer {
+    enabled = true
+    autoMounts = true
+    docker.enabled = false
+    pullTimeout = "3 hours"                // the default is 20 minutes and fails with large images
+    envWhitelist = 'CUDA_VISIBLE_DEVICES'  // allow the bounding of GPU visible device variable into the containers
+}
+
+process{
+    scratch = '$SCRATCHDIR'
+    maxRetries = 3
+    errorStrategy = { task.attempt<3 ? 'retry' : 'ignore' }
+    clusterOptions = '--no-requeue' //if slurm restarts a job nextflow doesnt always track it and resubmits anyway
+    cache = 'lenient'
+    afterScript = 'sleep 10'
+    queue = {
+        if ( task.time > 14.day ) {
+            "bigmem"
+        } else if ( task.memory > 256.GB ) {
+            "bigmem"
+        } else if task.memory / task.cpus <= 4 {
+            "htc-el8"
+        } else {
+            "bigmem"
+        }
+    }
+    withLabel:gpu {
+        queue = 'gpu-el8'
+        containerOptions = '--nv' //enable Nvidia support
+    }
+
+    withLabel:bigmem {
+        queue = 'bigmem'
+    }
+    withLabel: low_qos {
+        clusterOptions = '--qos=low --no-requeue'
+    }
+}
+
+executor {
+    name = "slurm"
+    queueSize = 400
+    submitRateLimit = "10/1sec"
+    exitReadTimeout = "30 min"
+    pollInterval = '10sec'
+    exitReadTimeout = "5 min"
+    retry.reason = "*"
+}

resources_to_s3_NF/tracks.csv

+assembly,trackID,name,type,category,description,path,is_text_index
+pmassv1_masked,annotation,Gene models,GTF,Annotation,Kevin's GTF file,/g/arendt/data/platynereis_massiliensis/genes/pmassv1.gtf,TRUE
+pmassv1_masked,emapper,EMAPPER models,GFF,Annotation,Kevin's GFF file from EMAPPER,/g/arendt/data/platynereis_massiliensis/proteome/pmassv1_EMAPPER.gff,FALSE
+pdumv021,annotation,Gene models,GTF,Annotation,Kevin's GTF file,/g/arendt/data/genome_assemblies/pdum-v2.1/genes/pdumv021.gtf,TRUE
+pdumv021,emapper,EMAPPER models,GFF,Annotation,Kevin's GFF file from EMAPPER,/g/arendt/data/genome_assemblies/pdum-v2.1/proteome/pdumv021_EMAPPER.emapper.gff,FALSE
+pdumv021,SN035_vcf,SN035,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN035.vcf",FALSE
+pdumv021,SN054_vcf,SN054,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN054.vcf",FALSE
+pdumv021,SN055_vcf,SN055,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN055.vcf",FALSE
+pdumv021,SN056_vcf,SN056,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN056.vcf",FALSE
+pdumv021,SN057_vcf,SN057,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN057.vcf",FALSE
+pdumv021,SN058_vcf,SN058,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_PlanetaryBiology/Variants_SN058.vcf",FALSE
+pdumv021,SN001_vcf,SN001,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN001.vcf",FALSE
+pdumv021,SN002_vcf,SN002,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN002.vcf",FALSE
+pdumv021,SN003_vcf,SN003,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN003.vcf",FALSE
+pdumv021,SN004_vcf,SN004,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN004.vcf",FALSE
+pdumv021,SN015_vcf,SN015,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN015.vcf",FALSE
+pdumv021,SN016_vcf,SN016,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN016.vcf",FALSE
+pdumv021,SN018_vcf,SN018,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN018.vcf",FALSE
+pdumv021,SN019_vcf,SN019,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN019.vcf",FALSE
+pdumv021,SN020_vcf,SN020,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN020.vcf",FALSE
+pdumv021,SN021_vcf,SN021,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN021.vcf",FALSE
+pdumv021,SN028_vcf,SN028,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN028.vcf",FALSE
+pdumv021,SN029_vcf,SN029,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN029.vcf",FALSE
+pdumv021,SN030_vcf,SN030,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN030.vcf",FALSE
+pdumv021,SN031_vcf,SN031,VCF,Variants,Tobi's variants,"/g/arendt/gerber/Processed_Files/Variants_Atlas/Variants_SN031.vcf",FALSE
+pdumv021,library_bam_1,Library 1,BAM,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/1.final.bam",FALSE
+pdumv021,library_bam_2,Library 2,BAM,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/2.final.bam",FALSE
+pdumv021,library_bam_3,Library 3,BAM,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/3.final.bam",FALSE
+pdumv021,library_bam_4,Library 4,BAM,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/4.final.bam",FALSE
+pdumv021,library_bam_5,Library 5,BAM,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/5.final.bam",FALSE
+pdumv021,library_bigwig_1,Library 1,BigWig,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/1.final.bam",FALSE
+pdumv021,library_bigwig_2,Library 2,BigWig,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/2.final.bam",FALSE
+pdumv021,library_bigwig_3,Library 3,BigWig,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/3.final.bam",FALSE
+pdumv021,library_bigwig_4,Library 4,BigWig,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/4.final.bam",FALSE
+pdumv021,library_bigwig_5,Library 5,BigWig,ATACseq,Lara's Snakemake outputs,"/g/arendt/Lara/8.FinalOutput/5.final.bam",FALSE
+pdumv021,SN073_15ng_collapsed,SN073 MASseq isoforms from the 15ng prep,GFF,MASseq,MASseq outputs from running isoseq collapse against the Pdum genome,"/scratch/cros/MASseq_output_new/SN073/collapsed.gff",FALSE
+pdumv021,SN073_60ng_collapsed,SN073 MASseq isoforms,GFF,MASseq,MASseq outputs from running isoseq collapse against the Pdum genome,"/scratch/cros/MASseq_output_new/SN073_60ng/collapsed.gff",FALSE