Merge branch 'master' into gis-branch

.github/workflows/main.yml

@@ -88,6 +88,8 @@ jobs:
           - "sanger"
           - "sbc_sharc"
           - "seg_globe"
+          - "tigem"
+          - "ucl_myriad"
           - "uct_hpc"
           - "unibe_ibu"
           - "uppmax"

README.md

@@ -142,6 +142,8 @@ Currently documentation is available for the following systems:
 - [SANGER](docs/sanger.md)
 - [SBC_SHARC](docs/sbc_sharc.md)
 - [SEG_GLOBE](docs/seg_globe.md)
+- [TIGEM](docs/tigem.md)
+- [UCL_MYRIAD](docs/ucl_myriad.md)
 - [UCT_HPC](docs/uct_hpc.md)
 - [UNIBE_IBU](docs/unibe_ibu.md)
 - [UPPMAX](docs/uppmax.md)
@@ -205,6 +207,8 @@ Currently documentation is available for the following pipelines within specific
   - [SBC_SHARC](docs/pipeline/atacseq/sbc_sharc.md)
 - chipseq
   - [SBC_SHARC](docs/pipeline/chipseq/sbc_sharc.md)
+- demultiplex
+  - [AWS_TOWER](docs/pipeline/demultiplex/aws_tower.md)
 - eager
   - [EVA](docs/pipeline/eager/eva.md)
 - mag

conf/munin.config

@@ -29,7 +29,7 @@ process {
 singularity {
   cacheDir   = '/data1/containers/'
   enabled    = true
-  runOptions = "--bind /media/BTB_2021_01"
+  //runOptions = "--bind /media/BTB_2021_01"
 }
 
 // To use docker, use nextflow run -profile munin,docker

conf/pipeline/atacseq/sbc_sharc.config

@@ -1,35 +1,33 @@
-/*
+// Sheffield Bioinformatics Core Configuration Profile - ShARC
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Custom Pipeline Resource Config for nf-core/atacseq
-              
-              Sheffield Bioinformatics Core Configuration Profile - ShARC
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-					
-                  Custom Pipeline Resource Config for nf-core/atacseq
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
 
 // process-specific resource requirements - reduced specification from those in atacseq/conf/base.config
 
 process {
 
+    // error and retry handling
+
+    errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
+    maxRetries = 2
+
+
+    // process labels
+
     withLabel:process_low {
         cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory' ) }
         time   = { check_max( 4.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_medium {
         cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 32.GB * task.attempt, 'memory' ) }
         time   = { check_max( 6.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_high {
         cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
-        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 128.GB * task.attempt, 'memory' ) }
         time   = { check_max( 8.h * task.attempt, 'time' ) }
     }
 
@@ -72,3 +70,4 @@ def check_max(obj, type) {
     }
   }
 }
+

conf/pipeline/chipseq/sbc_sharc.config

@@ -1,35 +1,33 @@
-/*
+// Sheffield Bioinformatics Core Configuration Profile - ShARC
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Custom Pipeline Resource Config for nf-core/chipseq
-              
-              Sheffield Bioinformatics Core Configuration Profile - ShARC
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-					
-                  Custom Pipeline Resource Config for nf-core/chipseq
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
 
 // process-specific resource requirements - reduced specification from those in chipseq/conf/base.config
 
 process {
+    
+    // error and retry handling
+
+    errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
+    maxRetries = 2
+
+
+    // process labels
 
     withLabel:process_low {
         cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory' ) }
         time   = { check_max( 4.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_medium {
         cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 32.GB * task.attempt, 'memory' ) }
         time   = { check_max( 6.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_high {
         cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
-        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 128.GB * task.attempt, 'memory' ) }
         time   = { check_max( 8.h * task.attempt, 'time' ) }
     }
 
@@ -72,3 +70,4 @@ def check_max(obj, type) {
     }
   }
 }
+

conf/pipeline/demultiplex/aws_tower.config

@@ -0,0 +1,29 @@
+// Profile config names for nf-core/configs
+
+params {
+  // Specific nf-core/configs params
+  config_profile_contact = 'Edmund Miller(@emiller88)'
+  config_profile_description = 'nf-core/demultiplex AWS Tower profile provided by nf-core/configs'
+}
+
+aws {
+   batch {
+      maxParallelTransfers = 24
+      maxTransferAttempts = 3
+   }
+   client {
+      maxConnections = 24
+      uploadMaxThreads = 24
+      maxErrorRetry = 3
+      socketTimeout = 3600000
+      uploadRetrySleep = 1000
+      uploadChunkSize = 32.MB
+   }
+}
+
+process {
+    withName: BASES2FASTQ {
+        cpus = 16
+        memory = 48.GB
+    }
+}

conf/pipeline/rnaseq/sbc_sharc.config

@@ -1,35 +1,33 @@
-/*
+// Sheffield Bioinformatics Core Configuration Profile - ShARC
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Custom Pipeline Resource Config for nf-core/rnaseq
-              
-              Sheffield Bioinformatics Core Configuration Profile - ShARC
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-					
-                  Custom Pipeline Resource Config for nf-core/rnaseq
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
 
 // process-specific resource requirements - reduced specification from those in rnaseq/conf/base.config
 
 process {
+    
+    // error and retry handling
+
+    errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
+    maxRetries = 2
+
+
+    // process labels
 
     withLabel:process_low {
         cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 12.GB * task.attempt, 'memory' ) }
         time   = { check_max( 4.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_medium {
         cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
-        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 32.GB * task.attempt, 'memory' ) }
         time   = { check_max( 6.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_high {
         cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
-        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 128.GB * task.attempt, 'memory' ) }
         time   = { check_max( 8.h * task.attempt, 'time' ) }
     }
 
@@ -38,7 +36,7 @@ process {
     }
 
     withLabel:process_high_memory {
-        memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 160.GB * task.attempt, 'memory' ) }
     }
 
 }

conf/pipeline/sarek/sbc_sharc.config

@@ -1,38 +1,33 @@
-/*
+// Sheffield Bioinformatics Core Configuration Profile - ShARC
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Custom Pipeline Resource Config for nf-core/sarek
-              
-              Sheffield Bioinformatics Core Configuration Profile - ShARC
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-                    
-                  Custom Pipeline Resource Config for nf-core/sarek
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
-
 
 // process-specific resource requirements - reduced specification from those in sarek/conf/base.config
 
 process {
-
     
+    // error and retry handling
+
+    errorStrategy = { task.exitStatus in [143,137,104,134,139,140,247] ? 'retry' : 'finish' }
+    maxRetries    = 2
+
+
     // process labels
 
     withLabel:process_low {
         cpus   = { check_max( 2 * task.attempt, 'cpus' ) }
-        memory = { check_max( 4.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
         time   = { check_max( 4.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_medium {
-        cpus   = { check_max( 4 * task.attempt, 'cpus' ) }
+        cpus   = { check_max( 6 * task.attempt, 'cpus' ) }
-        memory = { check_max( 8.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 72.GB * task.attempt, 'memory' ) }
         time   = { check_max( 6.h * task.attempt, 'time' ) }
     }
 
     withLabel:process_high {
-        cpus   = { check_max( 8 * task.attempt, 'cpus' ) }
+        cpus   = { check_max( 12 * task.attempt, 'cpus' ) }
-        memory = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 192.GB * task.attempt, 'memory' ) }
         time   = { check_max( 8.h * task.attempt, 'time' ) }
     }
 
@@ -41,7 +36,7 @@ process {
     }
 
     withLabel:process_high_memory {
-        memory = { check_max( 60.GB * task.attempt, 'memory' ) }
+        memory = { check_max( 240.GB * task.attempt, 'memory' ) }
     }
 
 
@@ -49,7 +44,7 @@ process {
 
     withName:'BWAMEM1_MEM|BWAMEM2_MEM' {
         cpus    = { check_max( 12 * task.attempt, 'cpus' ) }
-        memory  = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory  = { check_max( 192.GB * task.attempt, 'memory' ) }
         time    = { check_max( 8.h  * task.attempt, 'time' ) }
     }
 
@@ -66,11 +61,13 @@ process {
     }
 
     withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS' {
-        memory  = { check_max( 16.GB * task.attempt, 'memory' ) }
+        memory  = { check_max( 72.GB * task.attempt, 'memory' ) }
     }
 
     withName:'GATK4_MARKDUPLICATES' {
-        memory  = { check_max( 16.GB * task.attempt, 'memory' ) }
+        cpus    = { check_max( 12 * task.attempt, 'cpus' ) }
+        memory  = { check_max( 240.GB * task.attempt, 'memory' ) }
+        time    = { check_max( 12.h * task.attempt, 'time' ) }
     }
 
     withName:'FREEBAYES|SAMTOOLS_STATS|SAMTOOLS_INDEX|UNZIP' {

conf/sbc_sharc.config

@@ -1,39 +1,25 @@
-/*
+// Sheffield Bioinformatics Core Configuration Profile - ShARC
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+// Base Institutional Configuration
-              
-              Sheffield Bioinformatics Core Configuration Profile - ShARC
 
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-          
-                            Base Institutional Configuration
-
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
 
+// nf-core specific parameters displayed in header summary of each run
 
 params {
-  
-  // nf-core specific parameters displayed in header summary of each run
 
   config_profile_description = 'Sheffield Bioinformatics Core - ShARC'
   config_profile_contact = 'Lewis Quayle (l.quayle@sheffield.ac.uk)'
   config_profile_url = 'https://docs.hpc.shef.ac.uk/en/latest/sharc/index.html'
-  
-  // hpc resource limits
-
-  max_cpus = 16
-  max_memory = 64.GB
-  max_time = 96.h
 
 }
 
 
-// container engine
+// hpc resource limits
 
-singularity {
+params {
-
+  
-  enabled = true
+  max_cpus = 16
-  autoMounts = true
+  max_memory = 256.GB
+  max_time = 96.h
 
 }
 
@@ -47,11 +33,27 @@ process {
   executor = 'sge'
   penv = 'smp'
   queue = { task.time <= 6.h ? 'shortint.q' : 'all.q' }
-  clusterOptions = { "-l rmem=${task.memory.toGiga()}G" }
+  clusterOptions = { "-l rmem=${ (task.memory.toGiga() / task.cpus) }G" }
-
-  // error and retry handling
-
-  errorStrategy = { task.exitStatus in [143,137,104,134,139,140] ? 'retry' : 'finish' }
-  maxRetries = 2
 
 }
+
+
+// optional executor settings
+
+executor {
+
+  queueSize = 10
+  submitRateLimit = '1 sec'
+
+}
+
+
+// container engine
+
+singularity {
+
+  enabled = true
+  autoMounts = true
+
+}
+

conf/tigem.config

@@ -0,0 +1,14 @@
+params {
+  config_profile_description = 'Telethon Institute of Genetic and Medicine (TIGEM) provided by nf-core/configs.'
+  config_profile_contact = 'Giuseppe Martone (@giusmar)'
+  config_profile_url = 'https://github.com/giusmar'
+}
+
+process.executor = 'slurm'
+google.zone = 'europe-west1'
+
+singularity {
+    enabled = true
+    autoMounts = true
+    cacheDir = 'work/singularity'
+}

conf/ucl_myriad.config

@@ -0,0 +1,34 @@
+params {
+
+  config_profile_description = 'University College London Myriad cluster'
+  config_profile_contact = 'Chris Wyatt (ucbtcdr@ucl.ac.uk)'
+  config_profile_url = 'https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/'
+
+}
+
+process {
+  executor='sge'
+  penv = 'smp'
+}
+
+params {
+  // Defaults only, expecting to be overwritten
+  max_memory = 128.GB
+  max_cpus = 36
+  max_time = 72.h
+  // igenomes_base = 's3://ngi-igenomes/igenomes/'
+}
+
+// optional executor settings
+
+executor {
+
+  queueSize = 10
+  submitRateLimit = '1 sec'
+
+}
+
+singularity {
+    enabled = true
+    autoMounts = true
+}

conf/vsc_ugent.config

@@ -7,9 +7,11 @@ workDir = "$scratch_dir/work"
 // Perform work directory cleanup when the run has succesfully completed
 // cleanup = true
 
-// Reduce the job submit rate to about 5 per second, this way the server won't be bombarded with jobs
+// Reduce the job submit rate to about 3 per second, this way the server won't be bombarded with jobs
+// Limit queueSize to keep job rate under control and avoid timeouts
 executor {
     submitRateLimit = '3 sec'
+    queueSize = 50
 }
 
 // Specify that singularity should be used and where the cache dir will be for the images
@@ -114,4 +116,4 @@ profiles {
             scratch = "$scratch_dir"
         }
     }
-}
+}

docs/pipeline/demultiplex/aws_tower.md

@@ -0,0 +1,19 @@
+# nf-core/configs: AWS Tower Demultiplex specific configuration
+
+Extra specific configuration for demultiplex pipeline
+
+## Usage
+
+To use, run the pipeline with `-profile aws_tower`.
+
+This will download and launch the demultiplex specific [`aws_tower.config`](../../../conf/pipeline/demultiplex/aws_tower.config) which has been pre-configured with a setup suitable for AWS batch through tower.
+
+Example: `nextflow run nf-core/demultiplex -profile aws_tower`
+
+## eager specific configurations for eva
+
+Specific configurations for AWS has been made for demultiplex.
+
+### General profiles
+
+- The general AWS Tower profile runs with default nf-core/demultiplex parameters, but with modifications to account file transfer speed and optimized bases2fastq resources.

docs/tigem.md

@@ -0,0 +1,7 @@
+# nf-core/configs: TIGEM configuration
+
+To use, run the pipeline with `-profile tigem`. This will download and launch the tigem.config which has been pre-configured with a setup suitable for the TIGEM personal biocluster.
+
+---
+
+This configuration profile can be used on TIGEM clusters, with the pre-installed SLURM job scheduling system. An additional parameter is `google.zone` to allow downloading data from GCP for a specific time zone. It should not interfere with any local or other AWS configuration.

docs/ucl_myriad.md

@@ -0,0 +1,51 @@
+# nf-core/configs: Myriad Configuration
+
+All nf-core pipelines have been successfully configured for use on UCL's myriad cluster [University College London](https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/).
+
+To use, run the pipeline with `-profile ucl_myriad`. This will download and launch the [`ucl_myriad.config`](../conf/ucl_myriad.config) which has been pre-configured with a setup suitable for the myriad cluster. 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.
+
+## Using Nextflow on Myriad
+
+Before running the pipeline you will need to install and configure Nextflow and Singularity.
+
+### Singularity
+
+This can be done with the following commands:
+
+```bash
+## Load Singularity environment modules - these commands can be placed in your ~/.bashrc also
+module add java/openjdk-11/11.0.1
+module add singularity-env/1.0.0
+```
+
+Then set the correct configuration of the cache directories, where <YOUR_ID> is replaced with you credentials which you can find by entering `whoami` into the terminal once you are logged into myriad. Once you have added your credentials save these lines into your .bashrc file in the base directory (e.g. /home/<YOUR_ID>/.bashrc):
+
+```bash
+# Set all the Singularity cache dirs to Scratch
+export SINGULARITY_CACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/
+export SINGULARITY_TMPDIR=/home/<YOUR_ID>/Scratch/.singularity/tmp
+export SINGULARITY_LOCALCACHEDIR=/home/<YOUR_ID>/Scratch/.singularity/localcache
+export SINGULARITY_PULLFOLDER=/home/<YOUR_ID>/Scratch/.singularity/pull
+
+# Bind your Scratch directory so it is accessible from inside the container
+export SINGULARITY_BINDPATH=/scratch/scratch/<YOUR_ID>
+```
+
+### Nextflow
+
+Download the latest release of nextflow. Warning: the self-update line should update to the latest version, but sometimes not, so please check which is the latest release (https://github.com/nextflow-io/nextflow/releases), you can then manually set this by entering (`NXF_VER=XX.XX.X`).
+
+```bash
+## Download Nextflow-all
+curl -s https://get.nextflow.io | bash
+NXF_VER=22.10.0
+nextflow -self-update
+chmod a+x nextflow
+mv nextflow ~/bin/nextflow
+```
+
+Then make sure that your bin PATH is executable, by placing the following line in your .bashrc:
+
+```bash
+export PATH=$PATH:/home/<YOUR_ID>/bin
+```

docs/uppmax.md

@@ -8,7 +8,16 @@ We have a Slack channel dedicated to UPPMAX users on the nf-core Slack: [https:/
 
 ## Using the UPPMAX config profile
 
-Before running the pipeline you will need to either install `Nextflow` or load it using the environment module system (this can be done with e.g. `module load bioinfo-tools Nextflow/<VERSION>` where `VERSION` is e.g. `20.10`).
+The recommended way to activate `Nextflow`, `nf-core`, and any pipeline
+available in `nf-core` on UPPMAX is to use the [module system](https://www.uppmax.uu.se/resources/software/module-system/):
+
+```bash
+# Log in to the desired cluster
+ssh <USER>@{rackham,miarka,bianca}.uppmax.uu.se
+
+# Activate the modules, you can also choose to use a specific version with e.g. `Nextflow/21.10`.
+module load bioinfo-tools Nextflow nf-core nf-core-pipelines
+```
 
 To use, run the pipeline with `-profile uppmax` (one hyphen).
 This will download and launch the [`uppmax.config`](../conf/uppmax.config) which has been pre-configured with a setup suitable for the UPPMAX servers.
@@ -94,21 +103,13 @@ Before running a nf-core pipeline on `bianca` you will first have to download th
 In this guide, we use `rackham` to download and transfer files to the `wharf` area, but it can also be done on your own computer.
 If you use `rackham` to download the pipeline and the singularity containers, we recommend using an interactive session (cf [interactive guide](https://www.uppmax.uu.se/support/faq/running-jobs-faq/how-can-i-run-interactively-on-a-compute-node/)), which is what we do in the following guide.
 
+It is recommended to activate `Nextflow`, `nf-core` and your `nf-core`
+pipeline through the module system (see **Using the UPPMAX config profile**
+above). In case you need a specific version of any of these tools you can
+follow the guide below.
+
 ### Download and install Nextflow
 
-You can use the `Nextflow` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
-
-```bash
-# Connect to bianca
-$ ssh -A <USER>-<BIANCA_PROJECT>@bianca.uppmax.uu.se
-
-# See the available versions for the module
-module spider Nextflow
-
-# Load a specific version of the Nextflow module
-module load bioinfo-tools Nextflow/<VERSION>`
-```
-
 ```bash
 # Connect to rackham
 $ ssh -X <USER>@rackham.uppmax.uu.se
@@ -160,19 +161,6 @@ $ export NXF_SINGULARITY_CACHEDIR=/castor/project/proj_nobackup/singularity-imag
 
 ### Install nf-core tools
 
-You can use the `nf-core` UPPMAX provided `module`, but if necessary, you can also download a more recent version.
-
-```bash
-# Connect to rackham
-$ ssh -X <USER>@rackham.uppmax.uu.se
-
-# See the available versions for the module
-module spider nf-core
-
-# Load a specific version of the nf-core module
-module load bioinfo-tools nf-core/<VERSION>`
-```
-
 ```bash
 # Connect to rackham
 $ ssh -X <USER>@rackham.uppmax.uu.se
@@ -254,7 +242,7 @@ And then `nf-core/<PIPELINE>` can be used with:
 $ nextflow run ~/<PIPELINE> -profile uppmax --project <BIANCA_PROJECT> --genome <GENOME_ASSEMBLY> ...
 ```
 
-## Update a pipeline
+### Update a pipeline
 
 To update, repeat the same steps as for installing and update the link.
 

nfcore_custom.config

@@ -70,6 +70,8 @@ profiles {
   sanger       { includeConfig "${params.custom_config_base}/conf/sanger.config"}
   sbc_sharc    { includeConfig "${params.custom_config_base}/conf/sbc_sharc.config"}
   seg_globe    { includeConfig "${params.custom_config_base}/conf/seg_globe.config"}
+  tigem        { includeConfig "${params.custom_config_base}/conf/tigem.config"}
+  ucl_myriad   { includeConfig "${params.custom_config_base}/conf/ucl_myriad.config"}
   uct_hpc      { includeConfig "${params.custom_config_base}/conf/uct_hpc.config" }
   unibe_ibu    { includeConfig "${params.custom_config_base}/conf/unibe_ibu.config" }
   uppmax       { includeConfig "${params.custom_config_base}/conf/uppmax.config" }

pipeline/demultiplex.config

@@ -0,0 +1,13 @@
+/*
+ * -------------------------------------------------
+ *  nfcore/demultiplex custom profile Nextflow config file
+ * -------------------------------------------------
+ * Config options for custom environments.
+ * Cluster-specific config options should be saved
+ * in the conf/pipeline/demultiplex folder and imported
+ * under a profile name here.
+ */
+
+profiles {
+  aws_tower { includeConfig "${params.custom_config_base}/conf/pipeline/demultiplex/aws_tower.config" }
+}