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Parametrize vroom size #3

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Parametrize vroom size #3

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80536cc
parametrize vroom_size
franla23 Jun 11, 2024
05347b3
update readme
franla23 Jun 11, 2024
8d66130
add parameter to sequenza test
franla23 Jun 11, 2024
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7 changes: 5 additions & 2 deletions README.md
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Expand Up @@ -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 git@github.com:TRON-Bioinformatics/tronflow-copy-number-calling.git
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Good point, it would be good to have this in every tronflow repo, but this is obviously very difficult to maintain. Maybe we could have generic instructions when possible in the documentation and keep README files to a minimum. Just thinking aloud... maybe we can discuss in the larger group next week.


$ nextflow run main.nf -profile conda --input_files <YOUR_INPUT_FILE> --reference <YOUR_REFERENCE_FASTA> --intervals <YOUR_TARGET_REGIONS_BED> --tools cnvkit,sequenza
```

Expand All @@ -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)

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4 changes: 2 additions & 2 deletions local_modules/rsequenza/main.nf
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Expand Up @@ -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' }"
Expand All @@ -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")
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3 changes: 2 additions & 1 deletion tests/scripts/run_test_02.sh
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Expand Up @@ -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
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