implementation of goleft/indexcov #1312
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Candidate release 3.3.1
FEAT: Release Canditate 3.3.2
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| label 'process_single' | ||
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| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/goleft:0.2.4--h9ee0642_1': | ||
| 'biocontainers/goleft:0.2.4--h9ee0642_1' }" | ||
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| input: | ||
| val(meta) | ||
| path(bams) | ||
| path(fasta) | ||
| path(fai) | ||
| output: | ||
| path("${prefix}/*"),emit:output | ||
| path("versions.yml"),emit:versions | ||
| script: | ||
| def args = task.ext.args ?: '' | ||
| prefix = task.ext.prefix ?: "${meta.id}" | ||
| def input_files = bams.findAll{it.name.endsWith(".bam")} + bams.findAll{it.name.endsWith(".crai")} | ||
| def extranormalize = input_files.any{it.name.endsWith(".crai")} ? " --extranormalize " : "" | ||
| """ | ||
| goleft indexcov \\ | ||
| --fai "${fai}" \\ | ||
| --directory "${prefix}" \\ | ||
| ${extranormalize} \\ | ||
| $args \\ | ||
| ${input_files.join(" ")} | ||
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| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| goleft: \$(goleft --version 2>&1 | head -n 1 | sed 's/^.*goleft Version: //') | ||
| END_VERSIONS | ||
| """ |
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could you indent so it is similar to the other modules?
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| input: | ||
| val(meta) | ||
| path(bams) |
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is the tool run on all bams for all samples in one job?
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nevermind I see it further down. The docs say 30sec per 30 WGS 🤯 . Any idea how it scales with number of genomes?
nextflow_schema.json
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| @@ -100,7 +100,7 @@ | |||
| "fa_icon": "fas fa-toolbox", | |||
| "description": "Tools to use for duplicate marking, variant calling and/or for annotation.", | |||
| "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka2\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.", | |||
| "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$" | |||
| "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|sentieon_dedup|snpeff|strelka|tiddit|vep|indexcov)?,?)*(?<!,)$" | |||
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we need alphabetical sorting or Maxime won't let it pass 😄
| workflow BAM_GOLEFT_INDEXCOV { | ||
| take: | ||
| bam // channel: [mandatory] [ meta, bam, bai ] | ||
| fasta // channel: [mandatory] [ fasta ] |
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Suggested change
| fasta // channel: [mandatory] [ fasta ] | |
| fasta // channel: [mandatory] [ fasta ] |
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Hi, thank you for the review. FYI I currently don't have the time to work on this. I'll fix things later. |
No worries, we're getting a release ready, so this one will only be included in the next one |
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This is a preliminary PR to implement goleft/indexcov in sarek: https://nfcore.slack.com/archives/CE6SDEDAA/p1696931394165659 . For now I haven't looked at the indentation, syntax, doc, etc...
Basically the BAMs are re-indexed (see below) and collected into indexcov. The output of indexcov is a set of png, html, bed.gz, etc... files.
NEW FILE:
modules/local/samtools_index_for_indexcov/main.nfinstead of using the original bam files, I choose to re-index the bam, ignoring the unmapped, secondary, etc... It's quite fast as we only need a BAM header and a BAM index.NEW FILE:
modules/local/goleft/indexcov/main.nfthe process for indexcov itself. I know I should have used the nf-core/module I designed but somehow it was easier for me to handle the 'input:' from sarek. Also I don't know what is meta.id' in that context.NEW_FILE:
subworkflows/local/bam_goleft_indexcov/main.nfthe glue for the two processes above. I don't like that id:"PREFIX".NEW FILE:
modules/goleft.indexcov.configa config for goleft/indexcov . I cannot make it work: the publishDir, the files are currently not copied intoresultsNEW FILE:
modules/indexcov_reindex.configa config for re-indexing the bamMODIFIED:
subworkflows/local/bam_variant_calling_germline_all/main.nf. I only added the subworkflow for indexcov here, just after manta. I'm not sure it's the best place to insert it.MODIFIED:
conf/test_full_germline.config. I added indexcov to the list of toolsMODIFIED: nextflow_schema.json, same, I added indexcov in the pattern.MODIFIED: nextflow.config to include the configs above.
PR checklist
nf-core lint).nextflow run . -profile test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).