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Merge pull request nf-core#157 from ekushele/master
Output demultiplexed fast5 files
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,35 @@ | ||
| process DEMUX_FAST5 { | ||
| label 'process_medium' | ||
| publishDir "${params.outdir}", | ||
| mode: params.publish_dir_mode, | ||
| saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process)) } | ||
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| conda (params.enable_conda ? "bioconda:ont-fast5-api:4.0.0--pyhdfd78af_0" : null) | ||
| if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { | ||
| container "https://depot.galaxyproject.org/singularity/ont-fast5-api:4.0.0--pyhdfd78af_0" | ||
| } else { | ||
| container "quay.io/biocontainers/ont-fast5-api:4.0.0--pyhdfd78af_0" | ||
| } | ||
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| input: | ||
| path(input_path), stageAs: 'input_path/*' | ||
| tuple val(meta), path(input_summary) | ||
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| output: | ||
| path "demultiplexed_fast5/*" , emit: fast5 | ||
| path "versions.yml" , emit: versions | ||
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| script: | ||
| """ | ||
| demux_fast5 \\ | ||
| --input input_path \\ | ||
| --save_path ./demultiplexed_fast5 \\ | ||
| --summary_file $input_summary | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| demux_fast5: \$(echo \$(python -c\'import ont_fast5_api;print(ont_fast5_api.__version__)\')) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,62 +1,65 @@ | ||
| process GUPPY { | ||
| label 'process_medium' | ||
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| if (params.guppy_gpu) { | ||
| container = 'genomicpariscentre/guppy-gpu:4.0.14' | ||
| clusterOptions = params.gpu_cluster_options | ||
| } else { | ||
| container = 'genomicpariscentre/guppy:4.0.14' | ||
| } | ||
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| input: | ||
| path(input_path), stageAs: 'input_path/*' | ||
| val meta | ||
| path guppy_config | ||
| path guppy_model | ||
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| output: | ||
| path "fastq/*.fastq.gz" , emit: fastq | ||
| tuple val(meta), path("basecalling/*.txt") , emit: summary | ||
| path "basecalling/*" , emit: called | ||
| path "versions.yml" , emit: versions | ||
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| script: | ||
| def barcode_kit = params.barcode_kit ? "--barcode_kits $params.barcode_kit" : "" | ||
| def barcode_ends = params.barcode_both_ends ? "--require_barcodes_both_ends" : "" | ||
| def proc_options = params.guppy_gpu ? "--device $params.gpu_device --num_callers $task.cpus --cpu_threads_per_caller $params.guppy_cpu_threads --gpu_runners_per_device $params.guppy_gpu_runners" : "--num_callers 2 --cpu_threads_per_caller ${task.cpus/2}" | ||
| def config = "--flowcell $params.flowcell --kit $params.kit" | ||
| if (params.guppy_config) config = file(params.guppy_config).exists() ? "--config ./$guppy_config" : "--config $params.guppy_config" | ||
| def model = "" | ||
| if (params.guppy_model) model = file(params.guppy_model).exists() ? "--model ./$guppy_model" : "--model $params.guppy_model" | ||
| """ | ||
| guppy_basecaller \\ | ||
| --input_path input_path \\ | ||
| --save_path ./basecalling \\ | ||
| --records_per_fastq 0 \\ | ||
| --compress_fastq \\ | ||
| $barcode_kit \\ | ||
| $proc_options \\ | ||
| $barcode_ends \\ | ||
| $config \\ | ||
| $model | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| guppy: \$(echo \$(guppy_basecaller --version 2>&1) | sed -r 's/.{81}//') | ||
| END_VERSIONS | ||
| ## Concatenate fastq files | ||
| mkdir fastq | ||
| cd basecalling | ||
| if [ "\$(find . -type d -name "barcode*" )" != "" ] | ||
| then | ||
| for dir in barcode*/ | ||
| do | ||
| dir=\${dir%*/} | ||
| cat \$dir/*.fastq.gz > ../fastq/\$dir.fastq.gz | ||
| done | ||
| else | ||
| cat *.fastq.gz > ../fastq/${meta.id}.fastq.gz | ||
| fi | ||
| """ | ||
| label 'process_medium' | ||
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| if (params.guppy_gpu) { | ||
| container = 'genomicpariscentre/guppy-gpu:5.0.16' | ||
| clusterOptions = params.gpu_cluster_options | ||
| } else { | ||
| container = 'genomicpariscentre/guppy:5.0.16' | ||
| } | ||
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| input: | ||
| path(input_path), stageAs: 'input_path/*' | ||
| val meta | ||
| path guppy_config | ||
| path guppy_model | ||
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| output: | ||
| path "fastq/*.fastq.gz" , emit: fastq | ||
| tuple val(meta), path("basecalling/*.txt") , emit: summary | ||
| path "basecalling/*" , emit: called | ||
| path "versions.yml" , emit: versions | ||
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| script: | ||
| def trim_barcodes = params.trim_barcodes ? "--trim_barcodes" : "" | ||
| def barcode_kit = params.barcode_kit ? "--barcode_kits $params.barcode_kit" : "" | ||
| def barcode_ends = params.barcode_both_ends ? "--require_barcodes_both_ends" : "" | ||
| def proc_options = params.guppy_gpu ? "--device $params.gpu_device --num_callers $task.cpus --cpu_threads_per_caller $params.guppy_cpu_threads --gpu_runners_per_device $params.guppy_gpu_runners" : "--num_callers 2 --cpu_threads_per_caller ${task.cpus/2}" | ||
| def config = "--flowcell $params.flowcell --kit $params.kit" | ||
| if (params.guppy_config) config = file(params.guppy_config).exists() ? "--config ./$guppy_config" : "--config $params.guppy_config" | ||
| def model = "" | ||
| if (params.guppy_model) model = file(params.guppy_model).exists() ? "--model ./$guppy_model" : "--model $params.guppy_model" | ||
| """ | ||
| guppy_basecaller \\ | ||
| --input_path input_path \\ | ||
| --save_path ./basecalling \\ | ||
| --records_per_fastq 0 \\ | ||
| --compress_fastq \\ | ||
| $barcode_kit \\ | ||
| $proc_options \\ | ||
| $barcode_ends \\ | ||
| $config \\ | ||
| $model | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| guppy: \$(echo \$(guppy_basecaller --version 2>&1) | sed -r 's/.{81}//') | ||
| END_VERSIONS | ||
| ## Concatenate fastq files | ||
| mkdir fastq | ||
| cd basecalling | ||
| if [ "\$(find . -type d -name "barcode*" )" != "" ] | ||
| then | ||
| for dir in pass/barcode*/ | ||
| do | ||
| dir=\$(basename \${dir%*/}) | ||
| cat pass/\$dir/*.fastq.gz > ../fastq/\$dir.fastq.gz | ||
| done | ||
| else | ||
| cat *.fastq.gz > ../fastq/${meta.id}.fastq.gz | ||
| fi | ||
| """ | ||
| } |
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