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Merge pull request nf-core#40 from atrigila/add_tool_stitch
Add tool stitch
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1 +1,3 @@ | ||
| repository_type: pipeline | ||
| lint: | ||
| subworkflow_changes: false |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema", | ||
| "$id": "https://raw.githubusercontent.com/nf-core/phaseimpute/master/assets/schema_posfile.json", | ||
| "title": "nf-core/phaseimpute pipeline - params.posfile schema", | ||
| "description": "Schema for the file provided with params.posfile", | ||
| "type": "array", | ||
| "items": { | ||
| "type": "object", | ||
| "properties": { | ||
| "chr": { | ||
| "type": "string", | ||
| "pattern": "^\\S+$", | ||
| "errorMessage": "Chromosome name must be provided as a string and cannot contain spaces", | ||
| "meta": ["chr"] | ||
| }, | ||
| "file": { | ||
| "type": "string", | ||
| "pattern": "^\\S+\\.txt$", | ||
| "errorMessage": "Posfile per chromosome must be provided. Must have .txt extension" | ||
| } | ||
| }, | ||
| "required": ["chr", "file"] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,111 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Config file for defining DSL2 per module options and publishing paths | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| Available keys to override module options: | ||
| ext.args = Additional arguments appended to command in module. | ||
| ext.args2 = Second set of arguments appended to command in module (multi-tool modules). | ||
| ext.args3 = Third set of arguments appended to command in module (multi-tool modules). | ||
| ext.prefix = File name prefix for output files. | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
|
||
| process { | ||
|
|
||
| withName: CUSTOM_DUMPSOFTWAREVERSIONS { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/pipeline_info" }, | ||
| mode: params.publish_dir_mode, | ||
| pattern: '*_versions.yml' | ||
| ] | ||
| } | ||
|
|
||
| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/prep_panel/posfile/" }, | ||
| mode: params.publish_dir_mode, | ||
| enabled: true | ||
| ] | ||
| } | ||
|
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:GAWK' { | ||
| ext.args = "'{ key = \$1 FS \$2 } !seen[key]++'" | ||
| ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" } | ||
| ext.suffix = ".txt" | ||
| } | ||
|
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_NORM' { | ||
| ext.args = '-m +any --output-type z' | ||
| ext.prefix = { "${meta.id}_${meta.chr}_multiallelic" } | ||
| maxRetries = 2 | ||
| publishDir = [enabled: false] | ||
| } | ||
|
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_VIEW' { | ||
| ext.args = '-v snps -Oz' | ||
| ext.prefix = { "${meta.id}_${meta.chr}_biallelic" } | ||
| maxRetries = 2 | ||
| publishDir = [enabled: false] | ||
|
|
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| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_INDEX' { | ||
| maxRetries = 2 | ||
| publishDir = [enabled: false] | ||
|
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| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_INPUT_STITCH:BCFTOOLS_INDEX_2' { | ||
| ext.args = '--tbi' | ||
| maxRetries = 2 | ||
| publishDir = [enabled: false] | ||
|
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| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:PREPARE_POSFILE_TSV:BCFTOOLS_QUERY' { | ||
| ext.args = [ | ||
| "-f'%CHROM\t%POS\t%REF\t%ALT\\n'", | ||
| ].join(' ') | ||
| ext.prefix = { "${meta.id}_${meta.chr}_posfile_stitch" } | ||
| publishDir = [enabled: false] | ||
| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:.*' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/imputation/stitch/" }, | ||
| mode: params.publish_dir_mode, | ||
| enabled: true | ||
| ] | ||
| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:BAM_IMPUTE_STITCH:BCFTOOLS_INDEX' { | ||
| ext.args = '--tbi' | ||
| maxRetries = 2 | ||
| publishDir = [enabled: false] | ||
| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:.*' { | ||
| publishDir = [ | ||
| [ | ||
| path: { "${params.outdir}/imputation/stitch/concat" }, | ||
| mode: params.publish_dir_mode, | ||
| ], | ||
| ] | ||
| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_CONCAT' { | ||
| ext.args = {[ | ||
| "--ligate", | ||
| "--output-type z", | ||
| ].join(" ").trim()} | ||
| ext.prefix = { "${meta.id}_stitch" } | ||
| } | ||
|
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| withName: 'NFCORE_PHASEIMPUTE:PHASEIMPUTE:CONCAT_STITCH:BCFTOOLS_INDEX' { | ||
| ext.args = "--tbi" | ||
| ext.prefix = { "${meta.id}_stitch" } | ||
| } | ||
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|
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| } |
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