update modules in GATK's gcnvcaller pipeline #3561
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| Original file line number | Diff line number | Diff line change | ||||
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| @@ -1,9 +1,10 @@ | ||||||
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| process GATK4_DETERMINEGERMLINECONTIGPLOIDY { | ||||||
| tag "$meta.id" | ||||||
| label 'process_single' | ||||||
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| //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 | ||||||
| container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package | ||||||
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Quay.io is the default registry in all nf-core pipelines so we leave this out for more flexibility There was a problem hiding this comment. When I tried without it, singularity fails to pull the image. https://github.com/nf-core/modules/actions/runs/5394391319/jobs/9795497440 There was a problem hiding this comment. @adamrtalbot can you help with this? :) There was a problem hiding this comment. It's fixed in nf-core/tools#2336 but will require a new release. There was a problem hiding this comment. Also fixed with Nextflow version 23.04+ which includes There was a problem hiding this comment. Cool! I will let |
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| // Exit if running this module with -profile conda / -profile mamba | ||||||
| if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { | ||||||
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@@ -12,27 +13,25 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { | |||||
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| input: | ||||||
| tuple val(meta), path(counts), path(bed), path(exclude_beds) | ||||||
| tuple val(meta2), path(ploidy_model) | ||||||
| path(contig_ploidy_table) | ||||||
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| output: | ||||||
| tuple val(meta), path("${prefix}-calls"), emit: calls | ||||||
| tuple val(meta), path("${prefix}-model"), emit: model, optional: true | ||||||
| path "versions.yml" , emit: versions | ||||||
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| when: | ||||||
| task.ext.when == null || task.ext.when | ||||||
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| script: | ||||||
| def args = task.ext.args ?: '' | ||||||
| prefix = task.ext.prefix ?: "${meta.id}" | ||||||
| def intervals = bed ? "--intervals ${bed}" : "" | ||||||
| def exclude = exclude_beds ? exclude_beds.collect(){"--exclude-intervals $it"}.join(" ") : "" | ||||||
| def contig_ploidy = contig_ploidy_table ? "--contig-ploidy-priors ${contig_ploidy_table}" : "" | ||||||
| def model = ploidy_model ? "--model ${ploidy_model}" : "" | ||||||
| def input_list = counts.collect(){"--input $it"}.join(" ") | ||||||
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| def avail_mem = 3072 | ||||||
| if (!task.memory) { | ||||||
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@@ -41,8 +40,6 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { | |||||
| avail_mem = (task.memory.mega*0.8).intValue() | ||||||
| } | ||||||
| """ | ||||||
| gatk --java-options "-Xmx${avail_mem}M" DetermineGermlineContigPloidy \\ | ||||||
| ${input_list} \\ | ||||||
| --output ./ \\ | ||||||
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@@ -54,22 +51,17 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { | |||||
| --tmp-dir . \\ | ||||||
| ${args} | ||||||
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| cat <<-END_VERSIONS > versions.yml | ||||||
| "${task.process}": | ||||||
| gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') | ||||||
| END_VERSIONS | ||||||
| """ | ||||||
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| stub: | ||||||
| prefix = task.ext.prefix ?: "${meta.id}" | ||||||
| """ | ||||||
| touch ${prefix}-calls | ||||||
| touch ${prefix}-model | ||||||
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| cat <<-END_VERSIONS > versions.yml | ||||||
| "${task.process}": | ||||||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -21,6 +21,11 @@ input: | |
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - meta2: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - tsv: | ||
| type: file | ||
| description: One or more count TSV files created with gatk/collectreadcounts | ||
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@@ -31,12 +36,12 @@ input: | |
| pattern: "*.bed" | ||
| - model: | ||
| type: directory | ||
| description: Optional - directory containing the model produced by germlinecnvcaller cohort mode | ||
| pattern: "*-cnv-model/*-model" | ||
| - ploidy: | ||
| type: file | ||
| description: directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode | ||
| pattern: "*-calls" | ||
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| output: | ||
| - meta: | ||
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@@ -51,11 +56,11 @@ output: | |
| - calls: | ||
| type: file | ||
| description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode | ||
| pattern: "*-cnv-calls/*-calls" | ||
| - model: | ||
| type: directory | ||
| description: Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode | ||
| pattern: "*-cnv-model/*-model" | ||
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| authors: | ||
| - "@ryanjameskennedy" | ||
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| Original file line number | Diff line number | Diff line change | ||||
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@@ -3,36 +3,33 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { | |||||
| label 'process_single' | ||||||
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| //Conda is not supported at the moment: https://github.com/broadinstitute/gatk/issues/7811 | ||||||
| container "quay.io/nf-core/gatk:4.4.0.0" //Biocontainers is missing a package | ||||||
|
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Suggested change
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| // Exit if running this module with -profile conda / -profile mamba | ||||||
| if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { | ||||||
| exit 1, "GATK4_POSTPROCESSGERMLINECNVCALLS module does not support Conda. Please use Docker / Singularity / Podman instead." | ||||||
| } | ||||||
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| input: | ||||||
| tuple val(meta), path(ploidy, stageAs:'ploidy') | ||||||
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There was a problem hiding this comment. Why do you use There was a problem hiding this comment.
There was a problem hiding this comment. Ah we had long discussions about this in the past and decided to not use There was a problem hiding this comment. Ah, I see.. Alright I will change it 😄 |
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| tuple val(meta2), path(model) | ||||||
| tuple val(meta2), path(calls) | ||||||
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Suggested change
Same here |
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| output: | ||||||
| tuple val(meta), path("*_genotyped_intervals.vcf.gz") , emit: intervals, optional: true | ||||||
| tuple val(meta), path("*_genotyped_segments.vcf.gz") , emit: segments, optional: true | ||||||
| tuple val(meta), path("*_denoised.vcf.gz") , emit: denoised, optional: true | ||||||
| path "versions.yml" , emit: versions | ||||||
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| when: | ||||||
| task.ext.when == null || task.ext.when | ||||||
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| script: | ||||||
| def args = task.ext.args ?: '' | ||||||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||||||
| def ploidy_command = ploidy ? "--contig-ploidy-calls ${ploidy}" : "" | ||||||
| def model_command = model ? "--model-shard-path ${model}" : "" | ||||||
| def calls_command = calls ? "--calls-shard-path ${calls}" : "" | ||||||
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| def avail_mem = 3072 | ||||||
| if (!task.memory) { | ||||||
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@@ -41,10 +38,6 @@ process GATK4_POSTPROCESSGERMLINECNVCALLS { | |||||
| avail_mem = (task.memory.mega*0.8).intValue() | ||||||
| } | ||||||
| """ | ||||||
| gatk --java-options "-Xmx${avail_mem}g" PostprocessGermlineCNVCalls \\ | ||||||
| $ploidy_command \\ | ||||||
| $model_command \\ | ||||||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -21,23 +21,27 @@ input: | |
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - meta2: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. [ id:'test', single_end:false ] | ||
| - ploidy: | ||
| type: directory | ||
| description: | | ||
| Optional - A folder containing the ploidy model. | ||
| When a model is supplied to tool will run in CASE mode. | ||
| pattern: "*-calls/" | ||
| - calls: | ||
| type: directory | ||
| description: A folder containing the calls from the input files | ||
| pattern: "*-cnv-calls/*-calls" | ||
| - model: | ||
| type: directory | ||
| description: | | ||
| A folder containing the model from the input files. | ||
| This will only be created in COHORT mode (when no model is supplied to the process). | ||
| pattern: "*-cnv-model/*-model" | ||
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| output: | ||
| - meta: | ||
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