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valerianilucreziavalerianilucrezia
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Merge pull request #50 from caravagnalab/dev
Add stub nf-test + minor
2 parents 0a0538b + 34dbbff commit 3a74b3b

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‎docs/output.md‎

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@@ -134,7 +134,7 @@ This parser is designed to convert mutations data of joint CNAqc analysis from C
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## Lifter
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The Lifter subworkflow is an optional step and it is run when single sample VCF file are provided. When multiple samples from the same patient are provided, the user can specify either a single joint VCF file, containing variant calls from all tumor samples of the patient (see [joint variant calling](https://nf-co.re/sarek/3.4.2/parameters/#joint_mutect2)), or individual sample specific VCF files. In the latter case, path to tumor BAM files must be provided in order to collect all mutations from the samples and perform pile-up of sample's private mutations in all the other samples. Two intermediate steps, [get_positions](#get_positions) and [mpileup](#mpileup), are performed to identify private mutations in all the samples and retrieve their variant allele frequency. Once private mutations are properly defined, they are merged back into the original VCF file during the join_positions step. The updated VCF file is then converted into a RDS object.
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The Lifter subworkflow is an optional step, and it is run when, despite having multiple samples per patient, variant calling is performed separately on each sample. In this case, instead of a VCF file with a column per sample (multi-sample variant calling), a single VCF file is provided per sample. When multiple samples from the same patient are provided, the user can specify either a single joint VCF file, containing variant calls from all tumor samples of the patient (see [joint variant calling](https://nf-co.re/sarek/3.4.2/parameters/#joint_mutect2)), or individual sample specific VCF files. In the latter case, path to tumor BAM files must be provided in order to collect all mutations from the samples and perform pile-up of sample's private mutations in all the other samples. Two intermediate steps, [get_positions](#get_positions) and [mpileup](#mpileup), are performed to identify private mutations in all the samples and retrieve their variant allele frequency. Once private mutations are properly defined, they are merged back into the original VCF file during the join_positions step. The updated VCF file is then converted into a RDS object.
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### mpileup
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‎modules/local/annotate_driver/main.nf‎

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@@ -78,6 +78,18 @@ process ANNOTATE_DRIVER {
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writeLines(paste(" dplyr:", dplyr_version), f)
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writeLines(paste(" tidyr:", tidyr_version), f)
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close(f)
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_driver.rds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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readr: \$(Rscript -e "cat(as.character(packageVersion('readr')))")
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dplyr: \$(Rscript -e "cat(as.character(packageVersion('dplyr')))")
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tidyr: \$(Rscript -e "cat(as.character(packageVersion('tidyr')))")
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END_VERSIONS
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"""
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}

‎modules/local/cna2cnaqc/main.nf‎

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@@ -20,4 +20,15 @@ process CNA2CNAQC {
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script:
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template "main_script.R"
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.rds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnaqc: \$(Rscript -e "cat(as.character(packageVersion('CNAqc')))")
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END_VERSIONS
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"""
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}

‎modules/local/cnaqc2tsv/main.nf‎

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script:
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template "main_script.R"
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_joint_table.tsv
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnaqc: \$(Rscript -e "cat(as.character(packageVersion('CNAqc')))")
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readr: \$(Rscript -e "cat(as.character(packageVersion('readr')))")
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dplyr: \$(Rscript -e "cat(as.character(packageVersion('dplyr')))")
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END_VERSIONS
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"""
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}

‎modules/local/get_positions/main.nf‎

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@@ -40,4 +40,15 @@ process GET_POSITIONS_ALL {
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close(f)
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_all_positions.rds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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dplyr: \$(Rscript -e "cat(as.character(packageVersion('dplyr')))")
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END_VERSIONS
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"""
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}

‎modules/local/get_positions/main_rel.nf‎

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@@ -45,4 +45,14 @@ process GET_POSITIONS_REL {
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close(f)
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"""
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stub:
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"""
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touch ${meta.tumour_sample}_positions_missing
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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dplyr: \$(Rscript -e "cat(as.character(packageVersion('dplyr')))")
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END_VERSIONS
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"""
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}

‎modules/local/join_cnaqc/main.nf‎

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close(f)
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_multi_cnaqc_ALL.rds
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touch ${prefix}_multi_cnaqc_PASS.rds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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CNAqc: \$(Rscript -e "cat(as.character(packageVersion('CNAqc')))")
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dplyr: \$(Rscript -e "cat(as.character(packageVersion('dplyr')))")
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END_VERSIONS
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"""
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}

‎modules/local/join_positions/main.nf‎

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writeLines(paste(" vcfR:", vcfR_version), f)
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close(f)
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"""
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}_pileup_VCF.rds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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dplyr: \$(Rscript -e "cat(as.character(packageVersion('dplyr')))")
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tidyr: \$(Rscript -e "cat(as.character(packageVersion('tidyr')))")
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vcfR: \$(Rscript -e "cat(as.character(packageVersion('vcfR')))")
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END_VERSIONS
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"""
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}

‎modules/local/vcf2cnaqc/main.nf‎

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script:
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template "main_script.R"
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.rds
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cnaqc: \$(Rscript -e "cat(as.character(packageVersion('CNAqc')))")
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vcfR: \$(Rscript -e "cat(as.character(packageVersion('vcfR')))")
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dplyr: \$(Rscript -e "cat(as.character(packageVersion('dplyr')))")
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END_VERSIONS
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"""
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}

‎nextflow_schema.json‎

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},
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"genome": {
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"type": "string",
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"description": "Reference genome name."
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"description": "Reference genome name.",
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"enum": ["GRCh38", "GRCh37"]
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},
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"tools": {
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"type": "string",
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"publish_dir_mode_genome_sigprofiler": {
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"type": "string",
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"default": "move",
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"description": "Mode of publishing the SigProfiler genome."
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"description": "Mode of publishing the SigProfiler genome.",
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"enum": ["symlink", "rellink", "copy", "copyNoFollow", "move"]
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},
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"download_sigprofiler_genome": {
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"type": "boolean",

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