Merge pull request #45 from czbiohub/olgabot/czbiohub

[WIP] Add CZ Biohub

conf/czbiohub_aws.config

@@ -0,0 +1,111 @@
+/*
+ * -------------------------------------------------
+ *  Nextflow config file for Chan Zuckerberg Biohub
+ * -------------------------------------------------
+ * Defines reference genomes, using iGenome paths
+ * Imported under the default 'standard' Nextflow
+ * profile in nextflow.config
+ */
+
+ //Profile config names for nf-core/configs
+ params {
+   config_profile_description = 'Chan Zuckerberg Biohub AWS Batch profile provided by nf-core/configs.'
+   config_profile_contact = 'Olga Botvinnik (@olgabot)'
+   config_profile_url = 'https://www.czbiohub.org/'
+ }
+
+docker {
+  enabled = true
+}
+
+process {
+  executor = 'awsbatch'
+  queue = 'nextflow'
+}
+
+workDir = "s3://czb-nextflow/work"
+
+aws.region = 'us-west-2'
+executor.awscli = '/home/ec2-user/miniconda/bin/aws'
+params.tracedir = './'
+
+params {
+  saveReference = true
+
+  // Largest SPOT instances available on AWS: https://ec2instances.info/
+  max_memory = 1952.GB
+  max_cpus = 96
+  max_time = 240.h
+
+  // illumina iGenomes reference file paths on CZ Biohub reference s3 bucket
+  // No final slash because it's added later
+  igenomes_base = "s3://czbiohub-reference/igenomes"
+
+  // GENCODE (human + mouse) reference file paths on CZ Biohub reference s3 bucket
+  // No final slash because it's added later
+  gencode_base = "s3://czbiohub-reference/gencode"
+  transgenes_base = "s3://czbiohub-reference/transgenes"
+
+  // AWS configurations
+  awsregion = "us-west-2"
+  awsqueue = "nextflow"
+
+  // GENCODE GTF and fasta files
+  genomes {
+    'GRCh38' {
+      fasta   = "${params.gencode_base}/human/v29/GRCh38.p12.genome.fa"
+      gtf     = "${params.gencode_base}/human/v29/gencode.vM19.annotation.gtf"
+    }
+    'GRCm38' {
+      fasta   = "${params.gencode_base}/mouse/vM19/GRCm38.p6.genome.fa"
+      gtf     = "${params.gencode_base}/mouse/vM19/gencode.vM19.annotation.gtf"
+    }
+  }
+
+  transgenes {
+    'ChR2' {
+      fasta   = "${params.transgenes_base}/ChR2/ChR2.fa"
+      gtf     = "${params.transgenes_base}/ChR2/ChR2.gtf"
+    }
+    'Cre' {
+      fasta   = "${params.transgenes_base}/Cre/Cre.fa"
+      gtf     = "${params.transgenes_base}/Cre/Cre.gtf"
+    }
+    'ERCC' {
+      fasta   = "${params.transgenes_base}/ERCC92/ERCC92.fa"
+      gtf     = "${params.transgenes_base}/ERCC92/ERCC92.gtf"
+    }
+    'GCaMP6m' {
+      fasta   = "${params.transgenes_base}/GCaMP6m/GCaMP6m.fa"
+      gtf     = "${params.transgenes_base}/GCaMP6m/GCaMP6m.gtf"
+    }
+    'GFP' {
+      fasta   = "${params.transgenes_base}/Gfp/Gfp.fa"
+      gtf     = "${params.transgenes_base}/Gfp/Gfp.gtf"
+    }
+    'NpHR' {
+      fasta   = "${params.transgenes_base}/NpHR/NpHR.fa"
+      gtf     = "${params.transgenes_base}/NpHR/NpHR.gtf"
+    }
+    'RCaMP' {
+      fasta   = "${params.transgenes_base}/RCaMP/RCaMP.fa"
+      gtf     = "${params.transgenes_base}/RCaMP/RCaMP.gtf"
+    }
+    'RGECO' {
+      fasta   = "${params.transgenes_base}/RGECO/RGECO.fa"
+      gtf     = "${params.transgenes_base}/RGECO/RGECO.gtf"
+    }
+    'Tdtom' {
+      fasta   = "${params.transgenes_base}/Tdtom/Tdtom.fa"
+      gtf     = "${params.transgenes_base}/Tdtom/Tdtom.gtf"
+    }
+    'Car-T' {
+      fasta   = "${params.transgenes_base}/car-t/car-t.fa"
+      gtf     = "${params.transgenes_base}/car-t/car-t.gtf"
+    }
+    'zsGreen' {
+      fasta   = "${params.transgenes_base}/zsGreen/zsGreen.fa"
+      gtf     = "${params.transgenes_base}/zsGreen/zsGreen.gtf"
+    }
+  }
+}

docs/czbiohub.md

@@ -0,0 +1,141 @@
+# nf-core/configs: CZ Biohub Configuration
+
+All nf-core pipelines have been successfully configured for use on the AWS Batch at the Chan Zuckerberg Biohub here.
+
+To use, run the pipeline with `-profile czbiohub_aws`. This will download and launch the [`czbiohub_aws.config`](../conf/czbiohub_aws.config) which has been pre-configured with a setup suitable for the AWS Batch. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
+
+Ask Olga (olga.botvinnik@czbiohub.org) if you have any questions!
+
+## Run the pipeline from a small AWS EC2 Instance
+
+The pipeline will monitor and submit jobs to AWS Batch on your behalf. To ensure that the pipeline is successful, it will need to be run from a computer that has constant internet connection. Unfortunately for us, Biohub has spotty WiFi and even for short pipelines, it is highly recommended to run them from AWS. Make sure you have [aegea](https://github.com/czbiohub/codonboarding/blob/master/guides/aegea.md) installed to make launching AWS instances from the command line much easier.
+
+### 1. Launch the instance
+
+There is an Elastic Compute Cluster (EC2) Amazon machine image (AMI) set up with everything you need for Nextflow already installed. Its ID is `ami-091ec599f8e77734d` and can be launched from the command line with aegea like this:
+
+```
+aegea launch --iam-role S3fromEC2 -t t2.small --ami ami-091ec599f8e77734d --subnet subnet-672e832e $USER-nextflow
+```
+
+For example:
+
+```
+aegea launch --iam-role S3fromEC2 -t t2.small --ami ami-0adcc973d6f458a1e --subnet subnet-672e832e olgabot-nextflow
+```
+
+### 2. Log into the instance
+
+Log into the instance with `aegea ssh`:
+
+```
+aegea ssh ec2-user@$USER-nextflow
+```
+
+For a concrete example:
+
+```
+aegea ssh ec2-user@olgabot-nextflow
+```
+
+### 3. Start tmux
+
+[tmux](https://hackernoon.com/a-gentle-introduction-to-tmux-8d784c404340) is a "Terminal Multiplexer" that allows for commands to continue running even when you have closed your laptop and lost your connection. Start a new tmux session with `tmux new`
+
+```
+tmux new
+```
+
+Now you can run pipelines with abandon!
+
+### 4. Make a GitHub repo for your workflows (optional :)
+
+To make sharing your pipelines and commands easy between your teammates, it's best to share code in a GitHub repository. One way is to store the commands in a Makefile ([example](https://github.com/czbiohub/kh-workflows/blob/master/nf-kmer-similarity/Makefile)) which can contain multiple `nextflow run` commands so that you don't need to remember the S3 bucket or output directory for every single one. [Makefiles](https://kbroman.org/minimal_make/) are broadly used in the software community for running many complex commands. Makefiles can have a lot of dependencies and be confusing, so we're only going to write *simple* Makefiles.
+
+```
+rnaseq:
+  nextflow run -profile czbiohub_aws nf-core/rnaseq \
+      --reads 's3://czb-maca/Plate_seq/24_month/180626_A00111_0166_BH5LNVDSXX/fastqs/*{R1,R2}*.fastq.gz' \
+      --genome GRCm38 \
+      --outdir s3://olgabot-maca/nextflow-test/
+
+human_mouse_zebrafish:
+	nextflow run czbiohub/nf-kmer-similarity -latest -profile aws \
+		  --samples s3://kmer-hashing/hematopoeisis/smartseq2/human_mouse_zebrafish/samples.csv
+
+
+merkin2012_aws:
+	nextflow run czbiohub/nf-kmer-similarity -latest --sra "SRP016501" \
+		  -r olgabot/support-csv-directory-or-sra \
+		    -profile aws
+```
+
+In this example, one would run the `rnaseq` rule and the nextflow command beneath it with:
+
+```
+make rnaseq
+```
+
+If one wanted to run a different command, e.g. `human_mouse_zebrafish`, they would specify that command instead. For example:
+
+```
+make human_mouse_zebrafish
+```
+
+Makefiles are a very useful way of storing longer commands with short mnemonic words.
+
+
+Once you [create a new repository](https://github.com/organizations/czbiohub/repositories/new) (best to initialize with a `.gitignore`, license - MIT and `README`), clone that repository to your EC2 instance. For example, if the repository is called `kh-workflows`, this is what the command would look like:
+
+```
+git clone https://github.com/czbiohub/kh-workflows
+```
+
+Now both create and edit a `Makefile`:
+
+```
+cd
+nano Makefile
+```
+
+Write your rule with a colon after it, and on the next line must be a **tab**, not spaces. Once you're done, exit the program (the `^` command shown in nano means "Control"), write the file, add it to git, commit it, and push it up to GitHub.
+
+
+```
+git add Makefile
+git commit -m "Added makefile"
+git push origin master
+```
+
+
+### 5. Run your workflow!!
+
+Remember to specify `-profile czbiohub_aws` to grab the CZ Biohub-specific AWS configurations, and an `--outdir` with an AWS S3 bucket so you don't run out of space on your small AMI
+
+```
+nextflow run -profile czbiohub_aws nf-core/rnaseq \
+    --reads 's3://czb-maca/Plate_seq/24_month/180626_A00111_0166_BH5LNVDSXX/fastqs/*{R1,R2}*.fastq.gz' \
+    --genome GRCm38 \
+    --outdir s3://olgabot-maca/nextflow-test/
+```
+
+### 6. If you lose connection, how do you re-attach the tmux session?
+
+If you close your laptop, get onto the train, or lose WiFi connection, you may lose connection to your AWS EC2 instance. To reattach, use the command `tmux attach` and you should see your Nextflow output!
+
+```
+tmux attach
+```
+
+
+## iGenomes specific configuration
+
+A local copy of the iGenomes resource has been made available on `s3://czbiohub-reference` (in `us-west-2` region) so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
+You can do this by simply using the `--genome <GENOME_ID>` parameter.
+
+For Human and Mouse, we use [GENCODE](https://www.gencodegenes.org/) gene annotations. This doesn't change how you would specify the genome name, only that the pipelines run with the `czbiohub_aws` profile would be with GENCODE rather than iGenomes.
+
+
+>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT.
+
+>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.

nfcore_custom.config

@@ -16,6 +16,7 @@ profiles {
   ccga         { includeConfig "${params.custom_config_base}/conf/ccga.config" }
   cfc          { includeConfig "${params.custom_config_base}/conf/cfc.config" }
   crick        { includeConfig "${params.custom_config_base}/conf/crick.config" }
+  czbiohub_aws { includeConfig "${params.custom_config_base}/conf/czbiohub_aws.config" }
   gis          { includeConfig "${params.custom_config_base}/conf/gis.config" }
   hebbe        { includeConfig "${params.custom_config_base}/conf/hebbe.config" }
   mendel       { includeConfig "${params.custom_config_base}/conf/mendel.config" }