Sfitz add F8 and adjust F16 and F32 configs #256
There are no files selected for viewing
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,119 @@ | ||
| // Other processes will only run one at a time, so | ||
| // we don't need to control their resources. | ||
|
|
||
| process { | ||
| withName: run_validate_PipeVal { | ||
| cpus = 1 | ||
| memory = 1.GB | ||
| } | ||
| withName: call_sSNV_SomaticSniper { | ||
| cpus = 1 | ||
| memory = 1.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 2.GB | ||
| } | ||
| } | ||
| } | ||
| withName: convert_BAM2Pileup_SAMtools { | ||
| cpus = 1 | ||
| memory = 1.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 2.GB | ||
| } | ||
| } | ||
| } | ||
| withName: create_IndelCandidate_SAMtools { | ||
| cpus = 1 | ||
| memory = 1.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 2.GB | ||
| } | ||
| } | ||
| } | ||
| withName: call_sIndel_Manta { | ||
| cpus = 4 | ||
| memory = 3.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 3.GB | ||
| } | ||
| } | ||
| } | ||
| withName: call_sSNV_Strelka2 { | ||
| cpus = 4 | ||
| memory = 2.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 2.GB | ||
| } | ||
| } | ||
| } | ||
| withName: call_sSNV_Mutect2 { | ||
| cpus = 1 | ||
| memory = 3.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 2.GB | ||
| } | ||
| } | ||
| } | ||
| withName: run_LearnReadOrientationModel_GATK { | ||
| cpus = 1 | ||
| memory = 8.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'exponential' | ||
| operand = 2 | ||
| } | ||
| } | ||
| } | ||
| withName: call_sSNV_MuSE { | ||
| cpus = 4 | ||
| memory = 10.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 6.GB | ||
| } | ||
| } | ||
| } | ||
| withName: run_sump_MuSE { | ||
| cpus = 4 | ||
| memory = 12.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 4.GB | ||
| } | ||
| } | ||
| } | ||
| withName: plot_VennDiagram_R { | ||
| cpus = 2 | ||
| memory = 5.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 10.GB | ||
| } | ||
| } | ||
| } | ||
| withName: concat_VCFs_BCFtools { | ||
| cpus = 2 | ||
| memory = 5.GB | ||
| retry_strategy { | ||
| memory { | ||
| strategy = 'add' | ||
| operand = 10.GB | ||
| } | ||
| } | ||
| } | ||
| } |
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -54,7 +54,18 @@ if (params.max_cpus < 16 || params.max_memory < 30) { | |
| ------------------------------------ | ||
| ERROR: Insufficient resources: ${params.max_cpus} CPUs and ${params.max_memory} of memory. | ||
|
There was a problem hiding this comment. it seems you cited 'To run Mutect2 the pipeline requires at least 8 CPUs and 16 GB of memory', so I think the nested if block needs to be changed or updated depending on intended use. currently I think if you specify mutect2 and provide the cited resources it will error. I might suggest inverting these if blocks to check first for algorithm, and then check the resources meet the minimum requirement for the given algorithm. There was a problem hiding this comment. Oh good catch @kiarod. The first pair of cutoffs was supposed to be 8 and 16. It was accidentally reverted when I merged in the Do you think it's worth inverting the blocks? I think it would still require the same number of nested if statements and (trivially) would require evaluation of both every time. There was a problem hiding this comment. no worries! you're 100% right. Operationally they are the same thing, so your call on the if-blocks. The motivation for inverting the if-blocks was more so because the purpose of the if-blocks are to check sufficient resource requirement for specific algorithms, so in the case I suggested, there is one check per algorithm so it might be more straightforward to read/update/maintain, but no real performance difference especially considering these blocks are encountered once in a program that basically runs for a minimum of 2 hours haha There was a problem hiding this comment. I think there may be an advantage to this way in that the user is given relevant information for their resources. If it's done by algorithm they may have to fail twice before getting all the information. There was a problem hiding this comment. I noticed only one line of the error message was being printed, so I've updated them. |
||
| ------------------------------------ | ||
| To run Mutect2. this pipeline requires at least 8 CPUs and 16 GB of memory. | ||
| To run MuSE. this pipeline requires at least 16 CPUs and 32 GB of memory. | ||
| """ | ||
| } | ||
| } | ||
| else if (params.max_cpus < 16 || params.max_memory < 32) { | ||
| if (params.algorithm.contains('muse')) { | ||
| error """\ | ||
| ------------------------------------ | ||
| ERROR: Insufficient resources: ${params.max_cpus} CPUs and ${params.max_memory} of memory. | ||
| ------------------------------------ | ||
| To run MuSE. this pipeline requires at least 16 CPUs and 32 GB of memory. | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -5,4 +5,4 @@ Maintainers: ['[email protected]'] | |
| Contributors: ['Mao Tian', 'Bugh Caden', 'Helena Winata', 'Yash Patel', 'Sorel Fitz-Gibbon'] | ||
| Languages: ['Docker', 'Nextflow'] | ||
| Dependencies: ['Docker', 'Nextflow'] | ||
| Tools: ['GATK 4.4.0.0', 'SomaticSniper v1.0.5.0', 'Strelka2 v2.9.10', 'Manta v1.6.0', 'MuSE v2.0.4', 'BCFtools v1.17', 'R v4.3.1', 'VennDiagram v1.7.3', 'vcf2maf v1.6.18'] | ||
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
My concern here was that almost all users want to know what resources are required, but it was somewhat hidden under
Performance Validation.There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Yeah i think this is a good change, more clearly outlines what they can expect to find