Merge branch 'CW-3174' into 'dev'
No ref annotation workflow still completes Closes CW-3174 See merge request epi2melabs/workflows/wf-transcriptomes!154
This commit is contained in:
Sarah Griffiths
commit
84dbafd1c9
@ -52,7 +52,7 @@ docker-run:
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"fusions", "differential_expression", "isoforms",
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"only_differential_expression", "differential_expression_gff3",
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"ncbi_gzip", "ncbi_no_gene_id", "ensembl_with_versions",
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"differential_expression_mouse"
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"differential_expression_mouse", "no_ref_annotation"
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]
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rules:
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# NOTE As we're overriding the rules block for the included docker-run
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@ -66,6 +66,12 @@ docker-run:
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NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
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--ref_genome chr20/hg38_chr20.fa --ref_annotation chr20/gencode.v22.annotation.chr20.gtf --pychopper_backend phmm"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "no_ref_annotation"
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variables:
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NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz
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NF_WORKFLOW_OPTS: "--fastq ERR6053095_chr20.fastq --transcriptome-source reference-guided \
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--ref_genome chr20/hg38_chr20.fa"
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NF_IGNORE_PROCESSES: run_gffcompare,preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "fusions"
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variables:
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NF_BEFORE_SCRIPT: wget -O test_data.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/wf-isoforms_test_data.tar.gz && tar -xzvf test_data.tar.gz
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@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Add gene name column to the de_analysis counts TSV files.
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### Fixed
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- Mapping stage using a single thread only.
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- When no `--ref_annotation` is provided the workflow will still run but the output transcripts will not be annotated. However `--de_analysis` mode still requires a `--ref_annotation`.
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## [v1.0.0]
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### Added
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75
main.nf
75
main.nf
@ -323,8 +323,6 @@ process run_gffcompare{
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"""
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}
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process get_transcriptome{
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/*
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Write out a transcriptome file based on the query gff annotations.
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@ -340,6 +338,9 @@ process get_transcriptome{
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script:
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def transcriptome = "${sample_id}_transcriptome.fas"
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def merged_transcriptome = "${sample_id}_merged_transcriptome.fas"
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// if no ref_annotation gffcmp_dir will be optional file
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// so skip getting transcriptome FASTA from the annotated files.
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if (params.ref_annotation){
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"""
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gffread -g ${reference_seq} -w ${transcriptome} ${transcripts_gff}
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if [ "\$(ls -A $gffcmp_dir)" ];
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@ -347,6 +348,11 @@ process get_transcriptome{
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gffread -F -g ${reference_seq} -w ${merged_transcriptome} $gffcmp_dir/str_merged.annotated.gtf
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fi
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"""
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} else {
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"""
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gffread -g ${reference_seq} -w ${transcriptome} ${transcripts_gff}
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"""
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}
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}
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process merge_transcriptomes {
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@ -397,11 +403,11 @@ process makeReport {
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// for DE analysis, a `gene_name` column will be added to
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// `de_report/results_dge.tsv`
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path "results_dge.tsv", emit: de_analysis, optional: true
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script:
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shell:
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// Convert the sample_id arrayList.
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sids = new BlankSeparatedList(sample_ids)
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def report_name = "wf-transcriptomes-report.html"
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"""
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report_name = "wf-transcriptomes-report.html"
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'''
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if [ -f "de_report/OPTIONAL_FILE" ]; then
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dereport=""
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else
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@ -409,10 +415,14 @@ process makeReport {
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mv de_report/*.g*f* de_report/stringtie_merged.gtf
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fi
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if [ -f "gff_annotation/OPTIONAL_FILE" ]; then
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OPT_GFF=""
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OPT_GFF_ANNOTATION=""
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else
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OPT_GFF="--gffcompare_dir ${gffcmp_dir} --gff_annotation gff_annotation/*"
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OPT_GFF_ANNOTATION="--gff_annotation gff_annotation/*"
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fi
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if [ -f "OPTIONAL_FILE" ]; then
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OPT_GFFCMP_DIR=""
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else
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OPT_GFFCMP_DIR="--gffcompare_dir !{gffcmp_dir}"
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fi
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if [ -f "jaffal_csv/OPTIONAL_FILE" ]; then
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OPT_JAFFAL_CSV=""
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@ -429,18 +439,19 @@ process makeReport {
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else
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OPT_PC_REPORT="--pychop_report pychopper_report/*"
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fi
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workflow-glue report --report $report_name \
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--versions $versions \
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workflow-glue report --report !{report_name} \
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--versions !{versions} \
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--params params.json \
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\$OPT_ALN \
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\$OPT_PC_REPORT \
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--sample_ids $sids \
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${OPT_ALN} \
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${OPT_PC_REPORT} \
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--sample_ids !{sids} \
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--stats per_read_stats/* \
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\$OPT_GFF \
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--isoform_table_nrows $params.isoform_table_nrows \
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\$OPT_JAFFAL_CSV \
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\$dereport
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"""
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${OPT_GFF_ANNOTATION} \
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${OPT_GFFCMP_DIR} \
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--isoform_table_nrows !{params.isoform_table_nrows} \
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${OPT_JAFFAL_CSV} \
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${dereport}
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'''
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}
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@ -582,18 +593,28 @@ workflow pipeline {
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assemble_transcripts(split_bam.out.bundles.flatMap(map_sample_ids_cls).combine(ref_annotation),use_ref_ann)
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merge_gff_bundles(assemble_transcripts.out.gff_bundles.groupTuple())
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run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
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// only run gffcompare if ref annotation provided. Otherwise create optional files and channels
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if (params.ref_annotation){
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run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
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gff_compare_dir = run_gffcompare.out.gffcmp_dir
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gff_compare = run_gffcompare.out.gffcmp_dir.map{ it -> it[1]}.collect()
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// create per sample gff tuples with gff compare directories
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gff_tuple = merge_gff_bundles.out.gff
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.join(gff_compare_dir)
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} else {
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// create per sample gff tuples with optional files as no ref_annotation
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optional_channel = Channel.fromPath("$projectDir/data/OPTIONAL_FILE")
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gff_tuple = merge_gff_bundles.out.gff.combine(optional_channel)
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gff_compare = OPTIONAL_FILE
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}
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// For reference based assembly, there is only one reference
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// So map this reference to all sample_ids
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seq_for_transcriptome_build = sample_ids.flatten().combine(ref_genome)
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get_transcriptome(
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merge_gff_bundles.out.gff
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.join(run_gffcompare.out.gffcmp_dir)
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gff_tuple
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.join(seq_for_transcriptome_build))
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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 = results.concat(assembly.bam.map {sample_id, bam, bai -> [bam, bai]}.flatten())
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}
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@ -754,7 +775,7 @@ workflow {
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}
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if (params.de_analysis){
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if (!params.ref_annotation){
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error = "You must provide a reference annotation."
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error = "When running in --de_analysis mode you must provide a reference annotation."
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}
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if (!params.sample_sheet){
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error = "You must provide a sample_sheet with at least alias and condition columns."
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@ -762,6 +783,10 @@ workflow {
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if (params.containsKey("condition_sheet")) {
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error = "Condition sheets have been deprecated. Please add a 'condition' column to your sample sheet instead. Check the quickstart for more information."
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}
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} else{
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if (!params.ref_annotation){
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log.info("Warning: As no --ref_annotation was provided, the output transcripts will not be annotated.")
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}
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}
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if (error){
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throw new Exception(error)
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