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Get error estimation and pooled inference working
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,91 +1,64 @@ | ||
| // TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) | ||
| // https://github.com/nf-core/modules/tree/master/modules/nf-core/ | ||
| // You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: | ||
| // https://nf-co.re/join | ||
| // TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. | ||
| // All other parameters MUST be provided using the "task.ext" directive, see here: | ||
| // https://www.nextflow.io/docs/latest/process.html#ext | ||
| // where "task.ext" is a string. | ||
| // Any parameters that need to be evaluated in the context of a particular sample | ||
| // e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. | ||
| // TODO nf-core: Software that can be piped together SHOULD be added to separate module files | ||
| // unless there is a run-time, storage advantage in implementing in this way | ||
| // e.g. it's ok to have a single module for bwa to output BAM instead of SAM: | ||
| // bwa mem | samtools view -B -T ref.fasta | ||
| // TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty | ||
| // list (`[]`) instead of a file can be used to work around this issue. | ||
|
|
||
| process DADAINFER { | ||
| tag "$meta.id" | ||
| tag "$readmode" | ||
| label 'process_medium' | ||
|
|
||
| // TODO nf-core: List required Conda package(s). | ||
| // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). | ||
| // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. | ||
| // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. | ||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE': | ||
| 'biocontainers/YOUR-TOOL-HERE' }" | ||
| container "ghcr.io/h3abionet/tada:dev" | ||
|
|
||
| input: | ||
| // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" | ||
| // MUST be provided as an input via a Groovy Map called "meta". | ||
| // This information may not be required in some instances e.g. indexing reference genome files: | ||
| // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf | ||
| // TODO nf-core: Where applicable please provide/convert compressed files as input/output | ||
| // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. | ||
| tuple val(meta), path(bam) | ||
| tuple val(readmode), file(err), file(reads) | ||
|
|
||
| output: | ||
| // TODO nf-core: Named file extensions MUST be emitted for ALL output channels | ||
| tuple val(meta), path("*.bam"), emit: bam | ||
| // TODO nf-core: List additional required output channels/values here | ||
| path "versions.yml" , emit: versions | ||
| // path "versions.yml" , emit: versions | ||
| path("all.dd.${readmode}.RDS"), emit: inferred | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 | ||
| // If the software is unable to output a version number on the command-line then it can be manually specified | ||
| // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf | ||
| // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) | ||
| // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive | ||
| // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter | ||
| // using the Nextflow "task" variable e.g. "--threads $task.cpus" | ||
| // TODO nf-core: Please replace the example samtools command below with your module's command | ||
| // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) | ||
| def dadaOpt = !params.dadaOpt.isEmpty() ? "'${params.dadaOpt.collect{k,v->"$k=$v"}.join(", ")}'" : 'NA' | ||
| """ | ||
| samtools \\ | ||
| sort \\ | ||
| $args \\ | ||
| -@ $task.cpus \\ | ||
| -o ${prefix}.bam \\ | ||
| -T $prefix \\ | ||
| $bam | ||
| #!/usr/bin/env Rscript | ||
| suppressPackageStartupMessages(library(dada2)) | ||
| dadaOpt <- ${dadaOpt} | ||
| if (!is.na(dadaOpt)) { | ||
| setDadaOpt(dadaOpt) | ||
| cat("dada Options:\\n",dadaOpt,"\\n") | ||
| } | ||
| filts <- list.files('.', pattern="${readmode}.filtered.fastq.gz", full.names = TRUE) | ||
| err <- readRDS("${err}") | ||
| cat("Processing all samples\\n") | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| dadainfer: \$(samtools --version |& sed '1!d ; s/samtools //') | ||
| END_VERSIONS | ||
| #Variable selection from CLI input flag --pool | ||
| pool <- "${params.pool}" | ||
| # 'pool' is a weird flag, either 'pseudo' (string), or T/F (bool) | ||
| if(pool != "pseudo"){ | ||
| pool <- as.logical(pool) | ||
| } | ||
| dereps <- derepFastq(filts, n=100000, verbose=TRUE) | ||
| cat(paste0("Denoising ${readmode} reads: pool:", pool, "\\n")) | ||
| dds <- dada(dereps, err=err, multithread=${task.cpus}, pool=pool) | ||
| saveRDS(dds, "all.dd.${readmode}.RDS") | ||
| """ | ||
|
|
||
| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
|
|
||
| // TODO nf-core: A stub section should mimic the execution of the original module as best as possible | ||
| // Have a look at the following examples: | ||
| // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 | ||
| // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 | ||
| """ | ||
| touch ${prefix}.bam | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| dadainfer: \$(samtools --version |& sed '1!d ; s/samtools //') | ||
| END_VERSIONS | ||
| # add some real stuff here | ||
| touch all.dd.${readmode}.RDS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,91 +1,75 @@ | ||
| // TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :) | ||
| // https://github.com/nf-core/modules/tree/master/modules/nf-core/ | ||
| // You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace: | ||
| // https://nf-co.re/join | ||
| // TODO nf-core: A module file SHOULD only define input and output files as command-line parameters. | ||
| // All other parameters MUST be provided using the "task.ext" directive, see here: | ||
| // https://www.nextflow.io/docs/latest/process.html#ext | ||
| // where "task.ext" is a string. | ||
| // Any parameters that need to be evaluated in the context of a particular sample | ||
| // e.g. single-end/paired-end data MUST also be defined and evaluated appropriately. | ||
| // TODO nf-core: Software that can be piped together SHOULD be added to separate module files | ||
| // unless there is a run-time, storage advantage in implementing in this way | ||
| // e.g. it's ok to have a single module for bwa to output BAM instead of SAM: | ||
| // bwa mem | samtools view -B -T ref.fasta | ||
| // TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty | ||
| // list (`[]`) instead of a file can be used to work around this issue. | ||
|
|
||
| process LEARNERRORS { | ||
| tag "$meta.id" | ||
| label 'process_me' | ||
| tag "$readmode" | ||
| label 'process_medium' | ||
|
|
||
| // TODO nf-core: List required Conda package(s). | ||
| // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). | ||
| // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. | ||
| // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. | ||
| conda "${moduleDir}/environment.yml" | ||
| container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | ||
| 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE': | ||
| 'biocontainers/YOUR-TOOL-HERE' }" | ||
| container "ghcr.io/h3abionet/tada:dev" | ||
|
|
||
| input: | ||
| // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group" | ||
| // MUST be provided as an input via a Groovy Map called "meta". | ||
| // This information may not be required in some instances e.g. indexing reference genome files: | ||
| // https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf | ||
| // TODO nf-core: Where applicable please provide/convert compressed files as input/output | ||
| // e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc. | ||
| tuple val(meta), path(bam) | ||
| tuple val(readmode), file(reads) | ||
|
|
||
| output: | ||
| // TODO nf-core: Named file extensions MUST be emitted for ALL output channels | ||
| tuple val(meta), path("*.bam"), emit: bam | ||
| // TODO nf-core: List additional required output channels/values here | ||
| path "versions.yml" , emit: versions | ||
| // path "versions.yml" , emit: versions | ||
| tuple val(readmode), file("errors.${readmode}.RDS"), emit: error_models | ||
| // path("errors.R[12].RDS"), emit: errorModelsPerSample | ||
| path("${readmode}.err.pdf"), emit: pdf | ||
|
|
||
| when: | ||
| task.ext.when == null || task.ext.when | ||
|
|
||
| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10 | ||
| // If the software is unable to output a version number on the command-line then it can be manually specified | ||
| // e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf | ||
| // Each software used MUST provide the software name and version number in the YAML version file (versions.yml) | ||
| // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive | ||
| // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter | ||
| // using the Nextflow "task" variable e.g. "--threads $task.cpus" | ||
| // TODO nf-core: Please replace the example samtools command below with your module's command | ||
| // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;) | ||
| def prefix = task.ext.prefix | ||
| def derepreads = 100000 | ||
| // TODO: not even sure the below will work w/ nf-core style parameters, | ||
| // may need to go to a string or args-type modifications | ||
| def dadaOpt = !params.dadaOpt.isEmpty() ? "'${params.dadaOpt.collect{k,v->"$k=$v"}.join(", ")}'" : 'NA' | ||
| // TODO: will need to if-else this when implementing alternative error models | ||
| """ | ||
| samtools \\ | ||
| sort \\ | ||
| $args \\ | ||
| -@ $task.cpus \\ | ||
| -o ${prefix}.bam \\ | ||
| -T $prefix \\ | ||
| $bam | ||
| #!/usr/bin/env Rscript | ||
| suppressPackageStartupMessages(library(dada2)) | ||
| dadaOpt <- ${dadaOpt} | ||
| if (!is.na(dadaOpt)) { | ||
| setDadaOpt(dadaOpt) | ||
| cat("dada Options:\n",dadaOpt,"\n") | ||
| } | ||
| # File parsing (these come from the process input channel) | ||
| filts <- list.files('.', pattern=paste0("${readmode}",".filtered.fastq.gz"), full.names = TRUE) | ||
| sample.names <- sapply(strsplit(basename(filts), "_"), `[`, 1) # Assumes filename = samplename_XXX.fastq.gz | ||
| set.seed(100) | ||
| # Learn forward error rates | ||
| err <- learnErrors(filts, multithread=${task.cpus}, verbose=1) | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| learnerrors: \$(samtools --version |& sed '1!d ; s/samtools //') | ||
| END_VERSIONS | ||
| # This is a rough correction for NovaSeq binning issues | ||
| # See https://github.com/h3abionet/TADA/issues/31, we'll likely | ||
| # add alternatives here soon | ||
| if (as.logical("${params.quality_binning}") == TRUE ) { | ||
| # TODO: add alternatives for binning | ||
| print("Running binning correction") | ||
| errs <- t(apply(getErrors(err), 1, function(x) { x[x < x[40]] = x[40]; return(x)} )) | ||
| err\$err_out <- errs | ||
| } | ||
| pdf(paste0("${readmode}",".err.pdf")) | ||
| plotErrors(err, nominalQ=TRUE) | ||
| dev.off() | ||
| saveRDS(err, paste0("errors.","${readmode}",".RDS")) | ||
| """ | ||
|
|
||
| stub: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.id}" | ||
| def prefix = task.ext.prefix | ||
| // TODO nf-core: A stub section should mimic the execution of the original module as best as possible | ||
| // Have a look at the following examples: | ||
| // Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63 | ||
| // Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54 | ||
| """ | ||
| touch ${prefix}.bam | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| learnerrors: \$(samtools --version |& sed '1!d ; s/samtools //') | ||
| END_VERSIONS | ||
| # TODO: make a proper stub | ||
| """ | ||
| } |
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