deal with transcriptome fasta headers that contains |
This commit is contained in:
Sarah Griffiths
parent
36d37a8d5f
commit
edf3a24315
@ -45,7 +45,8 @@ docker-run:
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- MATRIX_NAME: [
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"fusions", "differential_expression", "isoforms",
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"only_differential_expression", "differential_expression_gff3",
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"ncbi_gzip", "denovo", "ncbi_no_gene_id", "ensembl_with_versions"
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"ncbi_gzip", "denovo", "ncbi_no_gene_id", "ensembl_with_versions",
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"differential_expression_mouse"
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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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@ -58,18 +59,18 @@ docker-run:
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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 --ref_annotation chr20/gencode.v22.annotation.chr20.gtf"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
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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 == "denovo"
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variables:
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NF_WORKFLOW_OPTS: "--fastq test_data/fastq/SIRV_E0_PCS109_50.fq.gz --transcriptome_source denovo"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,build_minimap_index
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref,build_minimap_index,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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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 \
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--jaffal_refBase chr20/ --jaffal_genome hg38_chr20 --jaffal_annotation genCode22"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
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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 == "differential_expression"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
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@ -78,7 +79,7 @@ docker-run:
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--ref_genome differential_expression/hg38_chr20.fa --transcriptome-source reference-guided \
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--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap2_index_opts '-k 15' --sample_sheet test_data/sample_sheet.csv"
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NF_IGNORE_PROCESSES: preprocess_reads,merge_transcriptomes,decompress_annotation,decompress_ref
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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 == "only_differential_expression"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
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@ -92,7 +93,7 @@ docker-run:
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--sample_sheet test_data/sample_sheet.csv"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "differential_expression_gff3"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
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@ -106,7 +107,7 @@ docker-run:
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--sample_sheet test_data/sample_sheet.csv"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,decompress_ref,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "ncbi_gzip"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz
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@ -120,7 +121,7 @@ docker-run:
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--sample_sheet test_data/sample_sheet.csv"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "ncbi_no_gene_id"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression_ncbi.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_ncbi.tar.gz && tar -xzvf differential_expression_ncbi.tar.gz
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@ -133,7 +134,7 @@ docker-run:
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--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "ensembl_with_versions"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression.tar.gz && tar -xzvf differential_expression.tar.gz
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@ -146,4 +147,17 @@ docker-run:
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--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam,decompress_transcriptome,preprocess_ref_transcriptome
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- if: $MATRIX_NAME == "differential_expression_mouse"
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variables:
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NF_BEFORE_SCRIPT: wget -O differential_expression_mouse.tar.gz https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-isoforms/differential_expression_mouse.tar.gz && tar -xzvf differential_expression_mouse.tar.gz
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NF_WORKFLOW_OPTS: "-executor.\\$$local.memory 16GB \
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--fastq differential_expression_mouse/differential_expression_fastq \
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--transcriptome-source precomputed --de_analysis \
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--ref_genome differential_expression_mouse/GRCm39.genome.fa.gz \
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--ref_annotation differential_expression_mouse/gencode.vM33.annotation.gtf \
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--direct_rna --ref_transcriptome differential_expression_mouse/gencode.vM33.transcripts.fa.gz \
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--transcriptome_assembly false --sample_sheet test_data/sample_sheet.csv"
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NF_IGNORE_PROCESSES: >
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preprocess_reads,merge_transcriptomes,assemble_transcripts,decompress_annotation,
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build_minimap_index,get_transcriptome,merge_gff_bundles,run_gffcompare,build_minimap_index,split_bam
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@ -4,6 +4,10 @@ All notable changes to this project will be documented in this file.
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
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and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
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## [v0.3.1]
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### Added
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- Handling for input reference transcriptome headers that contain `|`
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## [v0.3.0]
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### Changed
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- Improve differential expression outputs.
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@ -245,12 +245,13 @@ nextflow run epi2me-labs/wf-transcriptomes \
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--ref_transcriptome differential_expression/ref_transcriptome.fasta \
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--sample_sheet test_data/sample_sheet.csv
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```
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You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
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You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the `--transcriptome_source` to precomputed.
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eg.
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```
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nextflow run epi2me-labs/wf-transcriptomes \
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--fastq differential_expression/differential_expression_fastq \
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--de_analysis \
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--transcriptome_source precomputed \
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--ref_genome differential_expression/hg38_chr20.fa \
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--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap2_index_opts '-k 15' \
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@ -155,12 +155,13 @@ nextflow run epi2me-labs/wf-transcriptomes \
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--ref_transcriptome differential_expression/ref_transcriptome.fasta \
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--sample_sheet test_data/sample_sheet.csv
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```
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You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the transcriptome assembly parameter to false.
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You can also run the differential expression section of the workflow on its own by providing a reference transcriptome and setting the `--transcriptome_source` to precomputed.
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eg.
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```
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nextflow run epi2me-labs/wf-transcriptomes \
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--fastq differential_expression/differential_expression_fastq \
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--de_analysis \
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--transcriptome_source precomputed \
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--ref_genome differential_expression/hg38_chr20.fa \
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--ref_annotation differential_expression/gencode.v22.annotation.chr20.gtf \
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--direct_rna --minimap2_index_opts '-k 15' \
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35
main.nf
35
main.nf
@ -58,6 +58,7 @@ process getParams {
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}
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process decompress_ref {
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label "isoforms"
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cpus 1
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@ -83,6 +84,21 @@ process decompress_annotation {
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"""
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}
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process decompress_transcriptome {
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label "isoforms"
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cpus 1
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input:
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path "compressed_ref.gz"
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output:
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path "compressed_ref", emit: decompressed_ref
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"""
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gzip -df "compressed_ref.gz"
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"""
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}
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// Remove empty transcript ID fields
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process preprocess_ref_annotation {
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label "isoforms"
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@ -97,6 +113,21 @@ process preprocess_ref_annotation {
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"""
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}
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// Just keep transcript ID for each transcriptome fasta
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process preprocess_ref_transcriptome {
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label "isoforms"
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cpus 1
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input:
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path "ref_transcriptome"
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output:
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path "ammended.${ref_transcriptome}"
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"""
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sed -i -e 's/|.*//' ${ref_transcriptome}
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mv ${ref_transcriptome} "ammended.${ref_transcriptome}"
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"""
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}
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process preprocess_reads {
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/*
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@ -581,6 +612,10 @@ workflow pipeline {
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}
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else {
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transcriptome = Channel.fromPath(ref_transcriptome)
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if (file(params.ref_transcriptome).extension == "gz") {
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transcriptome = decompress_transcriptome(ref_transcriptome)
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}
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transcriptome = preprocess_ref_transcriptome(transcriptome)
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gtf = ref_annotation
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}
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de = differential_expression(transcriptome, input_reads, sample_sheet, gtf)
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