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Refactor #574
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Refactor #574
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4d74baf
remove skip_eklipse
ramprasadn d425660
Merge branch 'dev' of github.com:nf-core/raredisease into change-down…
ramprasadn a58d5ef
remove skip_haplocheck
ramprasadn cd583e4
remove skip_qualimap
ramprasadn 38edf8a
remove skip_fastqc
ramprasadn 391f8c9
add skip_smncopynumbercaller
ramprasadn 8101033
add skip for repeat annotation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,41 @@ | ||
| /* | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
| 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. | ||
| ext.when = Conditional clause | ||
| ---------------------------------------------------------------------------------------- | ||
| */ | ||
|
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| // | ||
| // Repeat expansion calling options | ||
| // | ||
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| process { | ||
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| withName: '.*ANNOTATE_REPEAT_EXPANSIONS:STRANGER' { | ||
| ext.prefix = { "${meta.id}_stranger" } | ||
| } | ||
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| withName: '.*ANNOTATE_REPEAT_EXPANSIONS:COMPRESS_STRANGER' { | ||
| ext.prefix = { "${meta.id}_repeat_expansion_stranger" } | ||
| ext.args = '--output-type z' | ||
| publishDir = [ | ||
| path: { "${params.outdir}/repeat_expansions" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| ] | ||
| } | ||
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| withName: '.*ANNOTATE_REPEAT_EXPANSIONS:INDEX_STRANGER' { | ||
| publishDir = [ | ||
| path: { "${params.outdir}/repeat_expansions" }, | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> filename.equals('versions.yml') ? null : filename }, | ||
| ] | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,34 @@ | ||
| // | ||
| // Annotate repeat expansions | ||
| // | ||
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| include { BCFTOOLS_VIEW as COMPRESS_STRANGER } from '../../modules/nf-core/bcftools/view/main' | ||
| include { STRANGER } from '../../modules/nf-core/stranger/main' | ||
| include { TABIX_TABIX as INDEX_STRANGER } from '../../modules/nf-core/tabix/tabix/main' | ||
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| workflow ANNOTATE_REPEAT_EXPANSIONS { | ||
| take: | ||
| ch_variant_catalog // channel: [mandatory] [ path(variant_catalog.json) ] | ||
| ch_vcf // channel: [mandatory] [ val(meta), path(vcf) ] | ||
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| main: | ||
| ch_versions = Channel.empty() | ||
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| // Annotate, compress and index | ||
| STRANGER ( ch_vcf, ch_variant_catalog ) | ||
| COMPRESS_STRANGER ( | ||
| STRANGER.out.vcf.map{ meta, vcf -> [meta, vcf, [] ]}, | ||
| [], [], [] | ||
| ) | ||
| INDEX_STRANGER ( COMPRESS_STRANGER.out.vcf ) | ||
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| ch_vcf_idx = COMPRESS_STRANGER.out.vcf.join(INDEX_STRANGER.out.tbi, failOnMismatch:true, failOnDuplicate:true) | ||
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| ch_versions = ch_versions.mix(STRANGER.out.versions.first()) | ||
| ch_versions = ch_versions.mix(COMPRESS_STRANGER.out.versions.first()) | ||
| ch_versions = ch_versions.mix(INDEX_STRANGER.out.versions.first()) | ||
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| emit: | ||
| vcf = ch_vcf_idx // channel: [ val(meta), path(vcf), path(tbi) ] | ||
| versions = ch_versions // channel: [ path(versions.yml) ] | ||
| } |
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So now neither the stub run nor the regular run of the downloaded pipeline is tested? As a user of an offline cluster, it's very nice to know that
nf-core downloadworks smoothly. But if there's no space maybe there's nothing to do.There was a problem hiding this comment.
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Yeah, that's right. The downloaded pipeline is not tested anymore. I can make sure that the downloaded pipeline works locally before a release, but the github runners just don't have enough space for both the downloaded containers and the tests :(