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Merge pull request #28 from karinlag/202207-v2
202207 v2
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,247 @@ | ||
| #!/usr/bin/env nextflow | ||
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| // This script is part of the Bifrost pipeline. Please see | ||
| // the accompanying LICENSE document for licensing issues, | ||
| // and the WIKI for this repo for instructions. | ||
|
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| // Which version do we have? | ||
| if (workflow.commitId) { | ||
| version = "v0.2.0 $workflow.revision" | ||
| } | ||
| else { | ||
| version = "v0.2.0 local" | ||
| } | ||
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| // TODO I need to incorporate some options for prokka here | ||
| // Also strip genome | ||
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| log.info '' | ||
| log.info "=================================================" | ||
| log.info " Bifrost assembly module version ${version}" | ||
| log.info "=================================================" | ||
| log.info "Reads : ${params.reads}" | ||
| log.info "#files in read set : ${params.setsize}" | ||
| log.info "Results can be found in : ${params.out_dir}" | ||
| log.info "=================================================" | ||
| log.info "" | ||
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| // First, define the input data that go into input channels | ||
| Channel | ||
| .fromFilePairs( params.reads, size:params.setsize ) | ||
| .ifEmpty { error "Cannot find any reads matching: ${params.reads}" } | ||
| .into{fastqc_reads; read_pairs} | ||
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| // run_fastq and run_multiqc are exactly the same as qc_track | ||
| process run_fastqc { | ||
| publishDir "${params.out_dir}/fastqc", mode: "${params.savemode}" | ||
| tag { pair_id } | ||
| label 'one' | ||
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| input: | ||
| set pair_id, file(reads) from fastqc_reads | ||
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| output: | ||
| file "$pair_id" into fastqc_results | ||
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| """ | ||
| mkdir ${pair_id} | ||
| fastqc -q ${reads} -o ${pair_id} -t $task.cpus | ||
| """ | ||
| } | ||
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| process run_multiqc { | ||
| publishDir "${params.out_dir}/multiqc", mode: "${params.savemode}" | ||
| tag {"multiqc"} | ||
| label 'one' | ||
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| input: | ||
| file "fastqc_output/*" from fastqc_results.toSortedList() | ||
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| output: | ||
| file "multiqc_report.html" into multiqc_report | ||
|
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| """ | ||
| multiqc fastqc_output | ||
| """ | ||
| } | ||
|
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| // if there are more than two data files, we need to cat them together | ||
| // because spades becomes complicated with more than two files | ||
| process collate_data { | ||
| // Note, not publishing these because that would mean | ||
| // triple copies of the files on the system | ||
| tag {pair_id} | ||
| label 'one' | ||
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| input: | ||
| set pair_id, file(reads) from read_pairs | ||
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| output: | ||
| set pair_id, file("${pair_id}*_concat.fq.gz") into (reads, pilon_reads) | ||
|
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| """ | ||
| cat ${pair_id}*R1* > ${pair_id}_R1_concat.fq.gz | ||
| cat ${pair_id}*R2* > ${pair_id}_R2_concat.fq.gz | ||
| """ | ||
| } | ||
|
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| /* | ||
| * Strip PhiX with bbmap | ||
| */ | ||
| process run_strip { | ||
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| publishDir "${params.out_dir}/bbduk", mode: "${params.savemode}" | ||
| tag { pair_id } | ||
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| input: | ||
| set pair_id, file(reads) from reads | ||
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| output: | ||
| set pair_id, file("${pair_id}*_concat_stripped.fq.gz") into reads_stripped | ||
| file "${pair_id}_bbduk_output.log" | ||
|
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| """ | ||
| bbduk.sh threads=$task.cpus ref=${params.stripgenome} \ | ||
| in1=${pair_id}_R1_concat.fq.gz \ | ||
| in2=${pair_id}_R2_concat.fq.gz \ | ||
| outm=${pair_id}_matched.fq.gz \ | ||
| out1=${pair_id}_R1_concat_stripped.fq.gz \ | ||
| out2=${pair_id}_R2_concat_stripped.fq.gz \ | ||
| k=31 hdist=1 stats=stats.txt &> ${pair_id}_bbduk_output.log | ||
| """ | ||
| } | ||
|
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|
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| /* | ||
| * Remove adapter sequences and low quality base pairs with Trimmomatic | ||
| */ | ||
| process run_trim { | ||
| publishDir "${params.out_dir}/bbduk_trimmed", mode: "${params.savemode}" | ||
| tag { pair_id } | ||
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| input: | ||
| set pair_id, file(reads) from reads_stripped | ||
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| output: | ||
| set pair_id, file("${pair_id}*_concat_stripped_trimmed.fq.gz") into reads_trimmed | ||
| file "${pair_id}_concat_stripped_trimmed.log" | ||
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| """ | ||
| trimmomatic PE -threads $task.cpus -trimlog ${pair_id}_concat_stripped_trimmed.log ${pair_id}*_concat_stripped.fq.gz \ | ||
| -baseout ${pair_id}_trimmed.fq.gz ILLUMINACLIP:${params.adapter_dir}/${params.adapters}:${params.illuminaClipOptions} \ | ||
| SLIDINGWINDOW:${params.slidingwindow} \ | ||
| LEADING:${params.leading} TRAILING:${params.trailing} \ | ||
| MINLEN:${params.minlen} &> ${pair_id}_run.log | ||
| mv ${pair_id}_trimmed_1P.fq.gz ${pair_id}_R1_concat_stripped_trimmed.fq.gz | ||
| mv ${pair_id}_trimmed_2P.fq.gz ${pair_id}_R2_concat_stripped_trimmed.fq.gz | ||
| cat ${pair_id}_trimmed_1U.fq.gz ${pair_id}_trimmed_2U.fq.gz > ${pair_id}_S_concat_stripped_trimmed.fq.gz | ||
| """ | ||
| } | ||
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| /* | ||
| * Build assembly with SPAdes | ||
| */ | ||
| process run_spadesasm { | ||
| publishDir "${params.out_dir}/spades", mode: "${params.savemode}" | ||
| tag { pair_id } | ||
| label 'longtime' | ||
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| input: | ||
| set pair_id, file(reads) from reads_trimmed | ||
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| output: | ||
| set pair_id, file("${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta") \ | ||
| into (assembly_results, tobwa_results) | ||
| file "${pair_id}_spades_scaffolds.fasta" | ||
| file "${pair_id}_spades.log" | ||
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| """ | ||
| spades.py ${params.careful} --cov-cutoff=${params.cov_cutoff} \ | ||
| -1 ${pair_id}_R1_concat_stripped_trimmed.fq.gz \ | ||
| -2 ${pair_id}_R2_concat_stripped_trimmed.fq.gz \ | ||
| -s ${pair_id}_S_concat_stripped_trimmed.fq.gz -t $task.cpus -o ${pair_id}_spades | ||
| filter_fasta_length.py -i ${pair_id}_spades/scaffolds.fasta \ | ||
| -o ${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta \ | ||
| -m ${params.min_contig_len} | ||
| cp ${pair_id}_spades/scaffolds.fasta ${pair_id}_spades_scaffolds.fasta | ||
| cp ${pair_id}_spades/spades.log ${pair_id}_spades.log | ||
| """ | ||
| } | ||
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| // integrate pilon. I need to have a mapping step, followed by a pilon | ||
| // step. | ||
|
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| /* | ||
| * Map reads to the spades assembly | ||
| */ | ||
| process run_bwamem { | ||
| publishDir "${params.out_dir}/bwamem", mode: "${params.savemode}" | ||
| tag { pair_id } | ||
| label 'longtime' | ||
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| input: | ||
| set pair_id, file("${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta"), \ | ||
| file(reads) from tobwa_results.join(pilon_reads) | ||
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| output: | ||
| set pair_id, file("${pair_id}_mapped_sorted.bam"), \ | ||
| file("${pair_id}_mapped_sorted.bam.bai") into bwamem_results | ||
|
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| """ | ||
| bwa index ${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta | ||
| bwa mem -t $task.cpus ${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta \ | ||
| *.fq.gz | samtools sort -o ${pair_id}_mapped_sorted.bam - | ||
| samtools index ${pair_id}_mapped_sorted.bam | ||
| """ | ||
| } | ||
|
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| /* | ||
| * Incorporating pilon_reads | ||
| */ | ||
|
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| process run_pilon { | ||
| publishDir "${params.out_dir}/pilon", mode: "${params.savemode}" | ||
| tag { pair_id } | ||
| label 'longtime' | ||
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| input: | ||
| set pair_id, file("${pair_id}_mapped_sorted.bam"), \ | ||
| file("${pair_id}_mapped_sorted.bam.bai"), \ | ||
| file("${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta") \ | ||
| from bwamem_results.join(assembly_results) | ||
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| output: | ||
| set pair_id, file("${pair_id}_pilon_spades.*") into pilon_results | ||
| file "${pair_id}_pilon_spades.fasta" into asms_for_quast | ||
|
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| """ | ||
| export _JAVA_OPTIONS=$task.javaopts | ||
| pilon --threads $task.cpus --genome ${pair_id}_spades_scaffolds_min${params.min_contig_len}.fasta \ | ||
| --bam ${pair_id}_mapped_sorted.bam --output ${pair_id}_pilon_spades \ | ||
| --changes --vcfqe &> ${pair_id}_pilon_spades.log | ||
| """ | ||
| } | ||
|
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| /* | ||
| * Evaluate ALL assemblies with QUAST | ||
| */ | ||
| process quast_eval { | ||
| // The output here is a directory in and of itself | ||
| // thus not creating a new one | ||
| publishDir "${params.out_dir}/", mode: "${params.savemode}" | ||
| tag { pair_id } | ||
|
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| input: | ||
| file asm_list from asms_for_quast.toSortedList() | ||
|
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| //TODO: fix this, is why output is not going anywhere | ||
| output: | ||
| file quast_evaluation_all into quast_evaluation_all | ||
|
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| """ | ||
| quast --threads $task.cpus -o quast_evaluation_all \ | ||
| -g ${params.quast_genes} -R ${params.quast_ref} ${asm_list} | ||
| """ | ||
| } |
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