Skip to content

tiny memory update + split fastq default value as discussed on slack #674

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
FriederikeHanssen merged 5 commits into from
Jul 21, 2022
Merged

tiny memory update + split fastq default value as discussed on slack #674

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
80e08d8
tiny memory update + split fastq default value as discussed on slack
FriederikeHanssen Jul 20, 2022
06e3f46
change log
FriederikeHanssen Jul 20, 2022
6bd0051
we don't have 50000000 test reads, so 0 for testing
FriederikeHanssen Jul 20, 2022
b63e4ee
only remove sharded number for duplicate marking, and only at the ver…
FriederikeHanssen Jul 20, 2022
6c7f310
no default, and ploidy is a number
FriederikeHanssen Jul 21, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -105,6 +105,7 @@ Skierfe is a mountain in the Sarek national park, and the inspiration for the lo
- [#661](https://github.com/nf-core/sarek/pull/661) - Add cnvkit reference creation to index subway map
- [#663](https://github.com/nf-core/sarek/pull/663) - Add separate parameters for `ASCAT` and `ControlFREEC` back in
- [#668](https://github.com/nf-core/sarek/pull/668) - Update annotation documentation
- [#674](https://github.com/nf-core/sarek/pull/664) - Default value for splitting is `50000000`

### Fixed

Expand Down
3 changes: 2 additions & 1 deletion assets/multiqc_config.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -61,7 +61,8 @@ extra_fn_clean_exts:

sample_names_replace_regex: True
sample_names_replace:
".[0-9]{4}": ".md"
"\\.[0-9]{4}$": ".md" # should match ".0001" but only at the end of strings for module Markduplicates/EstimateLibraryComplexity
module: picard

sp:
snpeff:
Expand Down
2 changes: 1 addition & 1 deletion conf/base.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ process {
withName: 'FASTP'{
cpus = { check_max( 12 * task.attempt, 'cpus' ) }
}
withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT|SAMTOOLS_MERGE'{
withName:'FASTQC|FASTP|MOSDEPTH|SAMTOOLS_CONVERT'{
memory = { check_max( 4.GB * task.attempt, 'memory' ) }
}
withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|SAMTOOLS_STATS'{
Expand Down
2 changes: 2 additions & 0 deletions conf/test.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -38,11 +38,13 @@ params {
snpeff_db = 'WBcel235.105'
snpeff_genome = 'WBcel235'
snpeff_version = '5.1'
split_fastq = 0
vep_cache_version = 106
vep_genome = 'WBcel235'
vep_species = 'caenorhabditis_elegans'
vep_version = '106.1'


// Ignore params that will throw warning through params validation
schema_ignore_params = 'genomes,test_data,snpeff_version,vep_version'
}
Expand Down
10 changes: 5 additions & 5 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,11 +20,11 @@ params {
save_reference = false // Built references not saved

// Main options
no_intervals = false // Intervals will be built from the fasta file
nucleotides_per_second = 1000 // Default interval size
tools = null // No default Variant_Calling or Annotation tools
skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default
split_fastq = 0 // FASTQ files will not be split by default by FASTP
no_intervals = false // Intervals will be built from the fasta file
nucleotides_per_second = 1000 // Default interval size
tools = null // No default Variant_Calling or Annotation tools
skip_tools = null // All tools (markduplicates + baserecalibrator + QC) are used by default
split_fastq = 50000000 // FASTQ files will not be split by default by FASTP

// Modify fastqs (trim/split) with FASTP
trim_fastq = false // No trimming
Expand Down
8 changes: 4 additions & 4 deletions nextflow_schema.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,7 @@
"properties": {
"split_fastq": {
"type": "integer",
"default": 0,
"default": 50000000,
"fa_icon": "fas fa-clock",
"description": "Specify how many reads each split of a FastQ file contains. Set 0 to turn off splitting at all.",
"help_text": "Use the the tool FastP to split FASTQ file by number of reads. This parallelizes across fastq file shards speeding up mapping. "
Expand Down Expand Up @@ -257,11 +257,11 @@
"help_text": "For more details, see [here](https://raw.githubusercontent.com/VanLoo-lab/ascat/master/man/ASCAT-manual.pdf)."
},
"ascat_ploidy": {
"type": "string",
"default": null,
"type": "number",
"fa_icon": "fas fa-bacon",
"help_text": "ASCAT: optional argument to override ASCAT optimization and supply psi parameter (expert parameter, don\u2019t adapt unless you know what you\u2019re doing). See [here](https://raw.githubusercontent.com/VanLoo-lab/ascat/master/man/ASCAT-manual.pdf)",
"hidden": true
"hidden": true,
"description": "Overwrite ASCAT ploidy."
},
"ascat_purity": {
"type": "number",
Expand Down
⚡