Parametrize vroom size

README.md

@@ -62,6 +62,9 @@ $ nextflow run tron-bioinformatics/tronflow-copy-number-calling -r <RELEASE|BRAN
 Option 2: Download the project and run it as follows...
 
 ```bash
+
+git clone --recurse-submodules [email protected]:TRON-Bioinformatics/tronflow-copy-number-calling.git
+
 $ nextflow run main.nf -profile conda --input_files <YOUR_INPUT_FILE> --reference <YOUR_REFERENCE_FASTA> --intervals <YOUR_TARGET_REGIONS_BED> --tools cnvkit,sequenza
 ```
 
@@ -87,13 +90,13 @@ Input:
     Example input file:
     name1	tumor_bam1	normal_bam1
     name2	tumor_bam2	normal_bam2
-    * reference: path to the FASTA genome reference
+    * reference: path to the FASTA genome reference. If sequenza is included, this file must not contain any alternative chromosomes and must be sorted in the same order as the bam file. 
     * intervals: path to the BED file with the targeted region
     * tools: tools to perform CN calling with (single and multiple entries possible, use ',' as delimiter) [ cnvkit, sequenza ]
 
 Optional input:
     * output: the folder where to publish output (default: output)
-    * VROOM_CONNECTION_SIZE: value for the environment variable VROOM_CONNECTION_SIZE which sometimes causes trouble with sequenza (default: 500000000)
+    * VROOM_CONNECTION_SIZE: value for the environment variable VROOM_CONNECTION_SIZE which sometimes causes trouble with sequenza and may need to be increased (default: 500000000)
     * cpus: the number of CPUs used by each job (default: 1)
     * memory: the amount of memory used by each job (default: 4g)
 

local_modules/rsequenza/main.nf

@@ -2,7 +2,7 @@ process R_SEQUENZA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "conda-forge::r-base=4.2.2 bioconda::r-sequenza=3.0.0" : null)
+    conda (params.enable_conda ? "conda-forge::r-base=4.2.2 bioconda::r-sequenza=3.0.0 conda-forge::r-iotools=0.3-2 " : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/r-sequenza:3.0.0--r42h3342da4_5' :
         'biocontainers/r-sequenza:3.0.0--r42h3342da4_5' }"
@@ -23,7 +23,7 @@ process R_SEQUENZA {
 
     library(sequenza)
 
-    Sys.setenv(VROOM_CONNECTION_SIZE = "131072000")
+    Sys.setenv(VROOM_CONNECTION_SIZE = "${params.VROOM_CONNECTION_SIZE}")
 
     seqz <- sequenza.extract(file="${seqz}", verbose = FALSE)
     #data.file <-  system.file("extdata", "example.seqz.txt.gz", package = "sequenza")

tests/scripts/run_test_02.sh

@@ -36,7 +36,8 @@ nextflow run main.nf \
 	--output ${output} \
 	--reference ${reference} \
 	--intervals ${intervals} \
-	--tools ${tool}
+	--tools ${tool} \
+	--VROOM_CONNECTION_SIZE 1536870912
 
 if [ $? -eq 1 ]
 then