Add quilt2 first draft implementation #282
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,42 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| */ | ||
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| process { | ||
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT2:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/imputation/quilt2/variant_calling/" }, | ||
| enabled: params.publish_all, | ||
| mode: params.publish_dir_mode, | ||
| ] | ||
| tag = {"Batch ${meta.batch} ${meta.regionout ?: meta.chr}"} | ||
| } | ||
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT2:QUILT_QUILT2' { | ||
| ext.args = "--seed=${params.seed}" | ||
| ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.quilt2" } | ||
| } | ||
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT2:GLIMPSE2_LIGATE' { | ||
| ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.chr}.quilt2.ligate" } | ||
| } | ||
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT2:BCFTOOLS_INDEX' { | ||
| ext.args = '--tbi' | ||
| } | ||
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT2:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/imputation/quilt2/concat" }, | ||
| mode: params.publish_dir_mode | ||
| ] | ||
| } | ||
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_QUILT2:BCFTOOLS_CONCAT' { | ||
| ext.args = "--output-type z --ligate" | ||
| ext.prefix = { "${meta.id}.batch${meta.batch}.quilt2" } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,44 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Nextflow config file for running minimal tests | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Defines input files and everything required to run a fast and simple pipeline test. | ||
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| Use as follows: | ||
| nextflow run nf-core/phaseimpute -profile test_quilt2,<docker/singularity> --outdir <OUTDIR> | ||
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| ---------------------------------------------------------------------------------------- | ||
| */ | ||
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| process { | ||
| resourceLimits = [ | ||
| cpus: 4, | ||
| memory: '4.GB', | ||
| time: '1.h' | ||
| ] | ||
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_QUILT2:QUILT_QUILT2' { | ||
| cpus = 1 | ||
| ext.args = {"--seed=${params.seed} --use_mspbwt=TRUE --impute_rare_common=FALSE" } | ||
| ext.prefix = { "${meta.id}.batch${meta.batch}.${meta.regionout ? meta.regionout.replace(':','_') : meta.chr}.quilt2" } | ||
| } | ||
| } | ||
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| params { | ||
| config_profile_name = 'Minimal QUILT2 Test profile' | ||
| config_profile_description = 'Minimal test dataset to check pipeline function using the tool QUILT2' | ||
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| // Input data | ||
| input = "${projectDir}/tests/csv/sample_bam.csv" | ||
| input_region = "${projectDir}/tests/csv/region.csv" | ||
| chunks = "${projectDir}/tests/csv/chunks.csv" | ||
| panel = "${projectDir}/tests/csv/panel.csv" | ||
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| // Genome references | ||
| fasta = params.pipelines_testdata_base_path + "hum_data/reference_genome/GRCh38.s.fa.gz" | ||
| map = "${projectDir}/tests/csv/map_glimpse.csv" | ||
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| // Pipeline parameters | ||
| steps = "impute" | ||
| tools = "quilt2" | ||
| } | ||
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