Merge branch 'CW-2369' into 'dev'
Resolve CW-2369 Closes CW-2369 See merge request epi2melabs/workflows/wf-transcriptomes!138
This commit is contained in:
Sarah Griffiths
commit
2580c99ae4
@ -6,6 +6,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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## [unreleased]
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### Added
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- Published minimap2 and pychopper results to output directory.
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- Two extra pychopper parameters `--cdna_kit` and `--pychopper_backend`. `--pychopper_options` is still available to define any other options.
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## [v0.4.2]
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46
main.nf
46
main.nf
@ -142,21 +142,32 @@ process preprocess_reads {
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cpus 4
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memory "2 GB"
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input:
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tuple val(meta), path(input_reads)
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tuple val(meta), path('seqs.fastq.gz')
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output:
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tuple val("${meta.alias}"), path("${meta.alias}_full_length_reads.fastq"), emit: full_len_reads
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path '*.tsv', emit: report
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tuple val("${meta.alias}"),
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path("${meta.alias}_pychopper_output/${meta.alias}_full_length_reads.fastq"),
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emit: full_len_reads
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tuple val("${meta.alias}"),
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path("${meta.alias}_pychopper_output/"),
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emit: pychopper_output
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path "${meta.alias}_pychopper_output/${meta.alias}_pychopper.tsv",
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emit: report
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script:
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def cdna_kit = params.cdna_kit.split("-")[-1]
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def extra_params = params.pychopper_opts ?: ''
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def extra_params = params.pychopper_opts ?: ''
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"""
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pychopper -t ${params.threads} -k ${cdna_kit} -m ${params.pychopper_backend} ${extra_params} ${input_reads} ${meta.alias}_full_length_reads.fastq
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pychopper -t ${params.threads} -k ${cdna_kit} -m ${params.pychopper_backend} ${extra_params} 'seqs.fastq.gz' ${meta.alias}_full_length_reads.fastq
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mv pychopper.tsv ${meta.alias}_pychopper.tsv
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workflow-glue generate_pychopper_stats --data ${meta.alias}_pychopper.tsv --output .
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# Add sample id column
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# Add sample id colum
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sed "1s/\$/\tsample_id/; 1 ! s/\$/\t${meta.alias}/" ${meta.alias}_pychopper.tsv > tmp
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mv tmp ${meta.alias}_pychopper.tsv
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mkdir "${meta.alias}_pychopper_output/"
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shopt -s extglob # Allow extended pattern matching so we can exclude files from the mv
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mv !("${meta.alias}_pychopper_output"|seqs.fastq.gz) "${meta.alias}_pychopper_output/"
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"""
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}
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@ -541,7 +552,7 @@ workflow pipeline {
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}
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results = Channel.empty()
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software_versions = getVersions()
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workflow_params = getParams()
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input_reads = reads.map{ meta, samples, stats -> [meta, samples]}
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@ -552,6 +563,8 @@ workflow pipeline {
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preprocess_reads(input_reads)
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full_len_reads = preprocess_reads.out.full_len_reads
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pychopper_report = preprocess_reads.out.report.collectFile(keepHeader: true)
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pychopper_results_dir = preprocess_reads.out.pychopper_output.map{ it -> it[1]}
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results = results.concat(pychopper_results_dir)
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}
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else{
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full_len_reads = input_reads.map{ meta, reads -> [meta.alias, reads]}
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@ -564,7 +577,7 @@ workflow pipeline {
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assembly_stats = assembly.stats.map{ it -> it[1]}.collect()
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split_bam(assembly.bam)
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split_bam(assembly.bam.map {sample_id, bam, bai -> [sample_id, bam]})
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assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls).combine(ref_annotation),use_ref_ann)
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@ -582,14 +595,14 @@ workflow pipeline {
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gff_compare = run_gffcompare.out.gffcmp_dir.map{ it -> it[1]}.collect()
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merge_gff = merge_gff_bundles.out.gff.map{ it -> it[1]}.collect()
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results = Channel.empty()
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}else
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{
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results = results.concat(assembly.bam.map {sample_id, bam, bai -> [bam, bai]}.flatten())
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}
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else{
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gff_compare = file("$projectDir/data/OPTIONAL_FILE")
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merge_gff = file("$projectDir/data/OPTIONAL_FILE")
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assembly_stats = file("$projectDir/data/OPTIONAL_FILE")
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use_ref_ann = false
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results = Channel.empty()
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}
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if (jaffal_refBase){
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gene_fusions(full_len_reads, jaffal_refBase, jaffal_genome, jaffal_annotation)
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@ -638,11 +651,9 @@ workflow pipeline {
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de_report,
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count_transcripts_file)
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report = makeReport.out.report
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results = results.concat(makeReport.out.report)
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report = makeReport.out.report
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results = results.concat(makeReport.out.report)
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if (use_ref_ann){
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results = run_gffcompare.output.gffcmp_dir.concat(
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@ -675,6 +686,7 @@ workflow pipeline {
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}
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results.concat(workflow_params.map{ [it, null]})
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emit:
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results
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@ -115,7 +115,6 @@ manifest {
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version = 'v0.4.2'
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}
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epi2melabs {
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tags = "isoforms, transcriptomics"
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}
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@ -12,18 +12,23 @@ process map_reads{
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tuple val(sample_id), path (fastq_reads), path(index), path(reference)
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output:
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tuple val(sample_id), path("${sample_id}_reads_aln_sorted.bam"), emit: bam
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tuple val(sample_id),
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path("${sample_id}_reads_aln_sorted.bam"),
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path("${sample_id}_reads_aln_sorted.bam.bai"),
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emit: bam
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tuple val(sample_id), path("${sample_id}_read_aln_stats.tsv"), emit: stats
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script:
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def ContextFilter = """AlnContext: { Ref: "${reference}", LeftShift: -${params.poly_context},
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RightShift: ${params.poly_context}, RegexEnd: "[Aa]{${params.max_poly_run},}",
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Stranded: True,Invert: True, Tsv: "internal_priming_fail.tsv"} """
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def mm2_threads = Math.min(task.cpus - 3, 1)
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"""
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minimap2 -t ${params.threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
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minimap2 -t ${mm2_threads} -ax splice ${params.minimap2_opts} ${index} ${fastq_reads}\
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| samtools view -q ${params.minimum_mapping_quality} -F 2304 -Sb -\
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| seqkit bam -j ${params.threads} -x -T '${ContextFilter}' -\
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| samtools sort -@ ${params.threads} -o "${sample_id}_reads_aln_sorted.bam" - ;
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((cat "${sample_id}_reads_aln_sorted.bam" | seqkit bam -s -j ${params.threads} - 2>&1) | tee ${sample_id}_read_aln_stats.tsv ) || true
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| seqkit bam -j 1 -x -T '${ContextFilter}' -\
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| samtools sort --write-index -@ 1 -o "${sample_id}_reads_aln_sorted.bam##idx##${sample_id}_reads_aln_sorted.bam.bai" - ;
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((cat "${sample_id}_reads_aln_sorted.bam" | seqkit bam -s -j 1 - 2>&1) | tee ${sample_id}_read_aln_stats.tsv ) || true
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if [[ -s "internal_priming_fail.tsv" ]];
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then
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